Entering edit mode
2.1 years ago
mohsamir2016
▴
30
Dear experts,
I would like to understand better the output of STAR log.final file alongside with samtools output:
I run STAR command without including --outSAMunmapped Within
and without outFilterMultimapNmax
nor outFilterMismatchNmax
, so this is default STAR:
I got statistics summary from the log.final file. my questions are:
- Are the number of input reads is exactly the same as the one that I have from trimmed versions of R1 and R2 summed up or?
- What exactly the Uniquely mapped reads number ? is that the n of reads that map to only 1 position on the genome OR that map to < 10 position OR the reads that do not have any other similar reads mapping to the position on the genome?
- Does the Uniquely mapped reads number include the multimapped reads that mapped tp < 10 position (so basically include the 'Number of reads mapped to multiple loci' appeared on statistics summary ?
- What does the reads with 255 mapping Q means? are these are the ones that map to only 1 place on the genome ? so should be equal to the number of Uniquely mapped reads number if it means mapped to 1 position (I tried that they are not the same? OR they are similar to the Uniquely mapped reads number if I set the
outFilterMultimapNmax
to 1 ?
Please could someone expert in STAR put an end to my confusion by elaboratively help me understating these points ?
Thanks