Question: Quick and easy way to get alignment stats from many SAM/BAM files?
0
gravatar for goodez
18 months ago by
goodez470
United States
goodez470 wrote:

Is there a good tool for extracting basic alignment stats from multiple BAMs/SAMs? I have tried CollectAlignmentSummaryMetrics from Picard and I really don't like it.

I just want simple statistics such as:

SAMPLE, TOTAL READS, ALIGNED READS, UNIQUELY MAPPED READS

It would be best if this were output in a table format so I could plot the statistics for many samples.

I could try to make a custom script for this, but I feel like a good tool should be out there.

rna-seq alignment • 1.4k views
ADD COMMENTlink modified 18 months ago • written 18 months ago by goodez470
1

So I am not the only one who dislikes the Picard tools :-D

ADD REPLYlink written 18 months ago by ATpoint28k
4
gravatar for genomax
18 months ago by
genomax76k
United States
genomax76k wrote:

Simply using samtools stats?

ADD COMMENTlink written 18 months ago by genomax76k
1

And samtools flagstat?

ADD REPLYlink modified 18 months ago • written 18 months ago by h.mon29k

Thanks -- not sure how I didn't come across this

ADD REPLYlink written 18 months ago by goodez470

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 18 months ago by WouterDeCoster42k
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