Question: Quick and easy way to get alignment stats from many SAM/BAM files?
0
gravatar for goodez
2.4 years ago by
goodez480
United States
goodez480 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 • 2.5k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by goodez480
1

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

ADD REPLYlink written 2.4 years ago by ATpoint41k
4
gravatar for genomax
2.4 years ago by
genomax92k
United States
genomax92k wrote:

Simply using samtools stats?

ADD COMMENTlink written 2.4 years ago by genomax92k
1

And samtools flagstat?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by h.mon31k

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

ADD REPLYlink written 2.4 years ago by goodez480

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 2.4 years ago by WouterDeCoster44k
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