HOw to check Tophat mapping stat / mapping rate

In the log folder inside the output folder,
look for bowtie.*.log

simplest way to know how many mapped:

samtools view accepted_hits.bam | cut -f1 | sort | uniq | wc -l

Actually,

The first round : bowtie.left_kept_reads.m2g_um.log

The second round : bowtie.left_kept_reads.m2g_um_unmapped.log