Question: Is there a tool for calculating the number of uniquely mapped reads, ambigiously mapped reads, and unmapped reads from sam/bam?
0
gravatar for O.rka
10 months ago by
O.rka230
O.rka230 wrote:

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 • 291 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by O.rka230
1

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 REPLYlink modified 10 months ago • written 10 months ago by lieven.sterck9.1k

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 REPLYlink written 10 months ago by O.rka230

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

ADD REPLYlink written 10 months ago by O.rka230

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

ADD REPLYlink written 10 months ago by cpad011214k

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

ADD REPLYlink written 10 months ago by GenoMax93k
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