Is there a tool for calculating the number of uniquely mapped reads, ambigiously mapped reads, and unmapped reads from sam/bam?
0
0
Entering edit mode
2.3 years ago
O.rka ▴ 540

I found a tool called MMQuant but this is suppose to be drop in replacement (though, it's not) for featureCounts. I'm trying to calculate the number of uniquely mapped reads, the number of ambigiously mapped reads, and the number of unmapped reads.

Is there a tool that can calculate these basic measures for sam/bam files?

RNA-Seq • 773 views
ADD COMMENT
1
Entering edit mode

why not just use featureCounts in the first place? (== might be useful to mention why do you want an alternative for it when asking for alternatives)

htseq-count ?

ADD REPLY
0
Entering edit mode

I’m getting a large number of ambiguously mapped reads and a very inconsistent gene expression between replicates. I suspect it’s a result of these ambiguous reads. I want to know exactly what proportion of the read pairs are ambiguously mapped.

ADD REPLY
0
Entering edit mode

I hadn't realized this information is in the summary output of featureCounts.

ADD REPLY
0
Entering edit mode

use combination of samtools and broad institute's website for flags

ADD REPLY
0
Entering edit mode

BBTools (reformat.sh has a number of stats options) for aligned data files.

ADD REPLY

Login before adding your answer.

Traffic: 2417 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6