Question: Add tags to BAM/SAM file
gravatar for dzb
11 months ago by
dzb0 wrote:

I'm working with some RNA-seq data. I have alignments done in STAR and the resultant BAM file. I'd like to annotate this BAM alignment data with custom tags using data that are stored in a separate file. The data in the second file contain are a read ID, a barcode, and a UMI. I want to add the barcode and UMI to all reads in the BAM file that match the read ID in the second file.

To summarise:

First file: BAM output from STAR

Second file: Read ID (matching those in STAR BAM file), UMI, barcode.

How do I get the UMI and barcode in file 2 tagged onto the reads in the BAM file?

Intensive Google and forum searching have yielded little info about this but I have a feeling there's a simple answer. Can anyone help?

ADD COMMENTlink modified 11 months ago by Matt Shirley8.4k • written 11 months ago by dzb0

Please post example lines from the two files.

ADD REPLYlink written 11 months ago by genomax49k
gravatar for Matt Shirley
11 months ago by
Matt Shirley8.4k
Cambridge, MA
Matt Shirley8.4k wrote:

I don't think there's a simple answer for this question, but if you want to write a script you might find simplesam ( useful:

ADD COMMENTlink written 11 months ago by Matt Shirley8.4k

This looks like an excellent starting point, thanks for sending it my way.

ADD REPLYlink written 10 months ago by dzb0
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