This error can be a serious one. Don't simply use the clipping solution suggested by some online threads.
Possible causes and solutions:
1. You mapped your reads to mm9 but used mm10 sizes to feed the bigBed generation script
Solution: use mm9 size file to redo the generation or map your reads to mm10
2. The program you used upstream extended the fragments and they exceeded the end
Solution: use bedClip for bed files and use -clip option for bedgraph files
Friday, September 30, 2016
Wednesday, September 28, 2016
How to turn off ios update reminder and especially automatic downloading
Settings -> General -> Storage & iCloud Usage -> Manage Storage -> tap on the ios update you want to skip and select delete
However, Apple will still try to find time to bring new ios update back to your phone again.
In order to stop them, you have to fill you phone with music or photos and leave less space than enough for the new update, so that they won't download any more.
reference:
http://osxdaily.com/2016/01/04/stop-ios-software-update-notification/
However, Apple will still try to find time to bring new ios update back to your phone again.
In order to stop them, you have to fill you phone with music or photos and leave less space than enough for the new update, so that they won't download any more.
reference:
http://osxdaily.com/2016/01/04/stop-ios-software-update-notification/
HOMER bug cannot create DNase/C2Dif: Is a directory
This occurs when you happen to have a folder with the same name as your bam file's name without the ".bam"
Solution: rename
Solution: rename
Monday, September 26, 2016
Caltech Swimming Class Journal
160926: Syllabus Rundown
Swimming suits needed:
swimoutlet.com
brief, jammer etc
160928: Water Safety
To float on water:
lay back onto water, relaxed
put head horizontal, facing the sky
Never look at the foot because that will make the head sink
To get off the floating state
move arms in the water closer to the body and push water upward
the body will get straight up
160930: move the legs
1. when floating on the back, do this practice:
put arms next to the body, head supported by a partner, whip the water with legs
always imagine the legs as whips. i.e. always move from the upper part of legs
2. use the kickboard
with back up, use two hands (2X4 fingers) to grab the front end of the board
use the legs to whip water
make sure the toes are balley 'ed straight
the highest point should be above water
high frequency, small amplitude
3. kick the wall
put dominant hand and the corresponding foot on the side of wall, the other hand on kickboard
Kick against the wall and move the hand on the wall up and onto the kickboard
161003: breathing
Back facing up
legs whiping: could bend knees to make sure laps are also moving
arms: upper arms and shoulders are stable, move forearms in the front < - -> and -> <-
hands: scoop water in and out
When moving arms out, you could take a breath by moving head gentle up and breathe in
When head in water, breathe out bubbles gently like playing a flute.
161005:breathing
Use kick boards to practice breathing
blow more bubbles in water
161010: backstroke
Practice 1: lay down in water with hands on the side, feet move like bicycling.
the highest point of the feet should be above water
Practice 2: lay down and move feet like Practice 1. Use palms to move back and forth. <- / \-> and \-> <- / Use palms to push water towards feet and body towards head.
Practice 3: lay down and move fee like Practice 1. put arms next to body, then move them along your body toward the shoulders, extend them to the right and left, and push water towards the feet till they reach your body. In this whole process the hands should be always below water.
161012:breaststroke
Legs:
put feet balley flat and move towards the chest, then extend bend feet to 90 degree to suddenly push water back and apart. The two legs shouldn't be close to the body when moving towards the chest.
Breath:
breath in air after the sudden push
Backstroke practice again:
When starting backstroke, slowly lay down to water and immediately start using arms to push water to avoid drowning at the first place
161017: backstroke kicking practice
put arms next to the body, the legs shouldn't be cycling but whiping using the force on hips. i.e., the knees shouldn't bend too much.
161019:backstroke and breaststroke
backstroke: this time, lift your straight arm up out of the water and get into water to push water towards the feet. One arm at a time.
When lifting, palms face inside. But when scooping water, palm facing outside.
Don't forget to move legs.
breaststroke: pay attention to the snap finish of feet
161021:backstroke
When starting backstroke, establish the kicks first.
The trick to keep floating: keep back straight and let the back of the neck press the water
161024:backstroke and breaststroke
backstroke: when putting down shoulders, remember to use neck to horizontally lift head up a little bit so that the face is above water.
breast stroke arm practice: put palms together like a buddhist, stick forward, open palms to push water backward, stop at the shoulder level and close the palms to finish the cycle; feet flutter kick
161026: free style
Flutter kick. Arms rotate and push water back
161028 and 161030: free style
It's important to keep the leading arm steady
Before taking down the leading arm, the other arm should have already been coming up.
When pulling down the arm, the body should be on its side
Practice swimming on the sides:
swimming on the side:
the leading arm is always straight.
it's very important to lay down the head to the leading arm so that we are able to get above the water when breathing in water, similar to Backstroke's principle.
When pulling out head to breath in air, we could breathe out the air/water from nose then breathe in air through mouth
161102: full backstroke and freestyle:
backstroke: make sure the body is on the water surface. Kicking should be stablized and use minimal knees bending
Try swimming a full 25 meters. When reaching the other end, grab the balloon.
freestyle: make sure the arms are always on opposite positions
when breathing in, swim on the side
161107: kick on the wall
practice kicking on the back and side and stomach, practice full backstroke
practice full free style (I can only breathe on my left side), every other stroke.
two arms always in opposite position
when breathing in, turn the head to look left-back-down, instead of just looking left and lifting it too much above water.
kicking on the wall:
1. use dominant hand to grab on the wall, two feet on the wall
2. dominant hand join the other hand, ventral on dorsal
3. kick against the wall
4. turn the body to stomach-down position
swim to the wall, grab up and kick and swim back.
161109: more about freestyle
opposite positions for two arms
Swim all the way to the other end!
breathe to the left side
Breathe more to better estimate lung storage
while in deep water and grabbing on the floating plastic, use legs to whip to balance
161114:continue working on freestyle
When breathing in, put head down onto the leading arm; look to the side of the pool instead of the feet.
Don't try to lift head up away from the leading arm.
161116:endurance training and backstroke
swim full 25 a couple times, with focus on body flipping training
Think of the arms as wings instead of wheels. push water towards the feet.
train kicking with boards for 25
161118: freestyle and breaststroke
freestyle: practice flipping body by using pull buoy
focus on sidebreath training
breastroke: different from backstroke and freestyle where bodyline should be straight, breaststroke and butterfly requires the body to swing front and back.
The feet are doing what hands would do in backstroke swim: bend through knees to lift feet, extend to the side and use the ventral/bottom of the feet to push water towards the posterior direction FROM the side, like wings instead of wheels or hand fan.
the two knees shouldn't be far from each other
While lifting the feet and extend to the sides, use arms to push water back and down and breathe
after arms' movement, do the sudden pushing of feet, and then bodyline becomes straight to glide without moving
161121: breaststroke
don't bend knees forward but lift legs backward while using the arms.
161128: freestyle and water safety
Freestyle: basic practice for scooping
Water safety:
1. treading water: feet flutter kick, arms scooping down water. Relax.
An easier way is to use feet to take turns to do breaststroke kick.
2. Flipping body: practice swim with freestyle, when swim on the side, flip to backstroke.
And practice flipping from backstroke to freestyle
161130: backstroke practice
practice grabbing water and pushing by doing chicken-soldier drill
Swim 100 yards by backstroke
Kickboard flutter kicking for 100 yards
Relaxing, going gentle and swinging like a fish really helps improve efficiency
161202: Swimming test
float on water for 3 min (on back)
backstroke 50 yards
Swimming suits needed:
swimoutlet.com
brief, jammer etc
160928: Water Safety
To float on water:
lay back onto water, relaxed
put head horizontal, facing the sky
Never look at the foot because that will make the head sink
To get off the floating state
move arms in the water closer to the body and push water upward
the body will get straight up
160930: move the legs
1. when floating on the back, do this practice:
put arms next to the body, head supported by a partner, whip the water with legs
always imagine the legs as whips. i.e. always move from the upper part of legs
2. use the kickboard
with back up, use two hands (2X4 fingers) to grab the front end of the board
use the legs to whip water
make sure the toes are balley 'ed straight
the highest point should be above water
high frequency, small amplitude
3. kick the wall
put dominant hand and the corresponding foot on the side of wall, the other hand on kickboard
Kick against the wall and move the hand on the wall up and onto the kickboard
161003: breathing
Back facing up
legs whiping: could bend knees to make sure laps are also moving
arms: upper arms and shoulders are stable, move forearms in the front < - -> and -> <-
hands: scoop water in and out
When moving arms out, you could take a breath by moving head gentle up and breathe in
When head in water, breathe out bubbles gently like playing a flute.
161005:breathing
Use kick boards to practice breathing
blow more bubbles in water
161010: backstroke
Practice 1: lay down in water with hands on the side, feet move like bicycling.
the highest point of the feet should be above water
Practice 2: lay down and move feet like Practice 1. Use palms to move back and forth. <- / \-> and \-> <- / Use palms to push water towards feet and body towards head.
Practice 3: lay down and move fee like Practice 1. put arms next to body, then move them along your body toward the shoulders, extend them to the right and left, and push water towards the feet till they reach your body. In this whole process the hands should be always below water.
161012:breaststroke
Legs:
put feet balley flat and move towards the chest, then extend bend feet to 90 degree to suddenly push water back and apart. The two legs shouldn't be close to the body when moving towards the chest.
Breath:
breath in air after the sudden push
Backstroke practice again:
When starting backstroke, slowly lay down to water and immediately start using arms to push water to avoid drowning at the first place
161017: backstroke kicking practice
put arms next to the body, the legs shouldn't be cycling but whiping using the force on hips. i.e., the knees shouldn't bend too much.
161019:backstroke and breaststroke
backstroke: this time, lift your straight arm up out of the water and get into water to push water towards the feet. One arm at a time.
When lifting, palms face inside. But when scooping water, palm facing outside.
Don't forget to move legs.
breaststroke: pay attention to the snap finish of feet
161021:backstroke
When starting backstroke, establish the kicks first.
The trick to keep floating: keep back straight and let the back of the neck press the water
161024:backstroke and breaststroke
backstroke: when putting down shoulders, remember to use neck to horizontally lift head up a little bit so that the face is above water.
breast stroke arm practice: put palms together like a buddhist, stick forward, open palms to push water backward, stop at the shoulder level and close the palms to finish the cycle; feet flutter kick
161026: free style
Flutter kick. Arms rotate and push water back
161028 and 161030: free style
It's important to keep the leading arm steady
Before taking down the leading arm, the other arm should have already been coming up.
When pulling down the arm, the body should be on its side
Practice swimming on the sides:
swimming on the side:
the leading arm is always straight.
it's very important to lay down the head to the leading arm so that we are able to get above the water when breathing in water, similar to Backstroke's principle.
When pulling out head to breath in air, we could breathe out the air/water from nose then breathe in air through mouth
161102: full backstroke and freestyle:
backstroke: make sure the body is on the water surface. Kicking should be stablized and use minimal knees bending
Try swimming a full 25 meters. When reaching the other end, grab the balloon.
freestyle: make sure the arms are always on opposite positions
when breathing in, swim on the side
161107: kick on the wall
practice kicking on the back and side and stomach, practice full backstroke
practice full free style (I can only breathe on my left side), every other stroke.
two arms always in opposite position
when breathing in, turn the head to look left-back-down, instead of just looking left and lifting it too much above water.
kicking on the wall:
1. use dominant hand to grab on the wall, two feet on the wall
2. dominant hand join the other hand, ventral on dorsal
3. kick against the wall
4. turn the body to stomach-down position
swim to the wall, grab up and kick and swim back.
161109: more about freestyle
opposite positions for two arms
Swim all the way to the other end!
breathe to the left side
Breathe more to better estimate lung storage
while in deep water and grabbing on the floating plastic, use legs to whip to balance
161114:continue working on freestyle
When breathing in, put head down onto the leading arm; look to the side of the pool instead of the feet.
Don't try to lift head up away from the leading arm.
161116:endurance training and backstroke
swim full 25 a couple times, with focus on body flipping training
Think of the arms as wings instead of wheels. push water towards the feet.
train kicking with boards for 25
161118: freestyle and breaststroke
freestyle: practice flipping body by using pull buoy
focus on sidebreath training
breastroke: different from backstroke and freestyle where bodyline should be straight, breaststroke and butterfly requires the body to swing front and back.
The feet are doing what hands would do in backstroke swim: bend through knees to lift feet, extend to the side and use the ventral/bottom of the feet to push water towards the posterior direction FROM the side, like wings instead of wheels or hand fan.
the two knees shouldn't be far from each other
While lifting the feet and extend to the sides, use arms to push water back and down and breathe
after arms' movement, do the sudden pushing of feet, and then bodyline becomes straight to glide without moving
161121: breaststroke
don't bend knees forward but lift legs backward while using the arms.
161128: freestyle and water safety
Freestyle: basic practice for scooping
Water safety:
1. treading water: feet flutter kick, arms scooping down water. Relax.
An easier way is to use feet to take turns to do breaststroke kick.
2. Flipping body: practice swim with freestyle, when swim on the side, flip to backstroke.
And practice flipping from backstroke to freestyle
161130: backstroke practice
practice grabbing water and pushing by doing chicken-soldier drill
Swim 100 yards by backstroke
Kickboard flutter kicking for 100 yards
Relaxing, going gentle and swinging like a fish really helps improve efficiency
161202: Swimming test
float on water for 3 min (on back)
backstroke 50 yards
Thursday, September 22, 2016
how to unsubscribe from Amazon Kindle unlimited [bug fixed]
I'm posting this not because the answer is hard to find, but because the official online answer is not quite right due to browser issues.
- Go to Manage your Kindle Unlimited Membership.
- Under Manage Membership select Cancel Kindle Unlimited Membership.
- Select End Membership on [DATE].
You would get stuck at Step 2 because the page you open will be blank.
The solution: use a cell phone, e.g. iphone safari browser works on that page.
Tuesday, September 20, 2016
What is DNA gel loading buffer?
Glycerol(dense and sticky) and bromophenol blue (dye for visualization)
more:
https://www.reference.com/science/function-loading-dye-electrophoresis-6527fb153da36b02#
http://openwetware.org/wiki/Agarose_gel_loading_dye
more:
https://www.reference.com/science/function-loading-dye-electrophoresis-6527fb153da36b02#
http://openwetware.org/wiki/Agarose_gel_loading_dye
Monday, September 19, 2016
[linux]how to list/ls the hidden files in a folder
ls -A for all the files
ls .* for all the files starting with a . that ls can't show
ls .* for all the files starting with a . that ls can't show
Tuesday, September 13, 2016
what is .io domain?
"""
British Indian Ocean Territory
he ccTLD (country code top level domain) and the internet country code for British Indian Ocean Territory
.IO can be used to substitute for the acronym i/o, or input/output
British Indian Ocean Territory
he ccTLD (country code top level domain) and the internet country code for British Indian Ocean Territory
.IO can be used to substitute for the acronym i/o, or input/output
About the British Indian Ocean Territory
Located in the Indian Ocean, the British Indian Ocean Territory is an archipelago south of India, about halfway between Africa and Indonesia. This area includes the entire Chagos Archipelago of 55 islands. The combined area of these islands is 21,004 square miles, about one third the size of Washington D.C. Currently there are no indigenous habitats on these islands. In the 1960's and 70's, approximately 1,200 former agricultural workers in the Chagos Archipelago were relocated to Mauritius and the Seychelles. In November 2000 they were granted the right of return by a British High Court ruling. However, this ruling was overturned in 2008, finding no right for the natives to return. By November 2004, approximately 4,000 United Kingdom and United States military personnel and civilian contractors were living on the island of Diego Garcia in a joint naval support facility.
There are no restrictions on .IO registrations
Anyone can register a .IO domain name, similar to .COM, .NET, or .ORG. To register a third-level .IO domain name you must be a resident of the British Indian Ocean Territory.
"""
reference: https://www.name.com/domains/io
Sunday, September 11, 2016
The mystery of the number 42
- If you google "the answer to the ultimate question of life the universe and everything", you'll see a calculator with 42 as the result.
- 42 is the result given by the web search engines Google and Wolfram Alpha when the query "the answer to life the universe and everything" is entered as a search.
import iphone contacts to Gmail/Google account on computer
1. log on iCloud using your computer
2. Go to contacts and select all of them
3. click the gear sign on the bottom left and export vCard and save
4. log onto google contacts (from google voice or gmail or calendar)
5. more -> import -> upload the contacts
6. Now go to your google voice/gmail, you will see the contacts updated
2. Go to contacts and select all of them
3. click the gear sign on the bottom left and export vCard and save
4. log onto google contacts (from google voice or gmail or calendar)
5. more -> import -> upload the contacts
6. Now go to your google voice/gmail, you will see the contacts updated
[Solved] Anaconda installed but can't simlink ; command not found
solution:
Close and reopen the terminal!
Friday, September 9, 2016
How to replace iphone 5c screen
0. I highly recommend you watch this video, although it's not perfect
1. I bought this screen repair kit
2. Don't lock your broken iphone 5c. Let the battery die over time
3. Take out the two screws here:
4. Use a tiny screw driver to insert in to the power hole and lift up the screen a little bit.
5. so that you could insert your guitar pick
6. and open the front plate
7. Now, you need to take off the screws holding the top right metal and take out the top right metal
8. Use the blue tool to unplug the front plate
9.Now you've taken the broken screen off.
10. put the new one back following the reverse order of this protocol.
1. I bought this screen repair kit
2. Don't lock your broken iphone 5c. Let the battery die over time
3. Take out the two screws here:
6. and open the front plate
8. Use the blue tool to unplug the front plate
New type of Phishing email targeting Caltech
From: Morgan719@caltech.edu
Dear phe,
Dear phe,
Please find attached documents as requested.
Best Regards,
Morgan
(Attached was a "Quarantined attachment")
Thursday, September 8, 2016
reorder two display screens on windows 7 / windows 8
1. right-click in a blank area on desktop
2. screen resolution
3. drag the two rectangle screens, click apply
4. click OK
2. screen resolution
3. drag the two rectangle screens, click apply
4. click OK
Wednesday, September 7, 2016
[imagej]how to count dots on an image
Two steps:
1. using a threshold to convert your image into binary form (positive + negative)
Image ▶ Adjust ▶ Threshold.
check "dark background"
Drag the bars so that the thresholds let the particles/dots stand out while leaving no background smears there
2. If your dots have overlapping groups, force them to separate:
Process ▶ Binary ▶ Watershed.
3. Analyze Particles
size: 0-infinity or leave blank
More stringent: 10-infinity
Analyze ▶ Analyze particles
Show: -> Eclipse
check display results and summarize
reference:
http://imagej.net/Particle_Analysis
1. using a threshold to convert your image into binary form (positive + negative)
Image ▶ Adjust ▶ Threshold.
check "dark background"
Drag the bars so that the thresholds let the particles/dots stand out while leaving no background smears there
2. If your dots have overlapping groups, force them to separate:
Process ▶ Binary ▶ Watershed.
3. Analyze Particles
size: 0-infinity or leave blank
More stringent: 10-infinity
Analyze ▶ Analyze particles
Show: -> Eclipse
check display results and summarize
reference:
http://imagej.net/Particle_Analysis
Tuesday, September 6, 2016
[Solved]How to unsubscribe from Caltech Marketplace email list
"1. Click on the link at the bottom of each message (https://lists.caltech.edu/lis
2. Using the email address that is subscribed to this list, send an email tomarketplace-leave@caltech.edu. It doesn't matter what you put in the subject line or body of the email (you can leave it blank). Use this option if you are away from Caltech and have no way of getting onto the Caltech network.
"
--- HN
Thursday, September 1, 2016
trimmomatic ILLUMINACLIP: how to specify an universal path for adaptor sequences file
A bug for ILLUMINACLIP 0.33:
They always add a prefix of locations which is the current path, before the file name you provide. Therefore it assumes that the adaptor file is in the current folder, which is not always true.
In order to specify a universal location, you can just specify the full path and activate its full path read mode. e.g. /usr/data/adaptors.fa
ATTENTION: never use ~ as home because it's not recognized by trimmomatic 0.33
They always add a prefix of locations which is the current path, before the file name you provide. Therefore it assumes that the adaptor file is in the current folder, which is not always true.
In order to specify a universal location, you can just specify the full path and activate its full path read mode. e.g. /usr/data/adaptors.fa
ATTENTION: never use ~ as home because it's not recognized by trimmomatic 0.33
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