RiboTaper

A copy RiboTaper v1.3.1a and some debugs by myself.

The original RiboTaper is in here.

Notice

P-site definition

RiboTaper takes only 10% reads for P-site definition. But it is poor for the case with low seq depth.

So, I adjust to 100% to adapt to all kinds of situations.

best & unique BAM

We could see from source script Ribotaper.sh

samtools view -b -q 50 $ribo_bam > RIBO_unique.bam 
samtools view -b -F 0X100 $ribo_bam > RIBO_best.bam 

It is ok for STAR aligner.

bug fixed

1.quality_check.R line 114 & 118