convert unmapped bam to fastqs and preserve tag
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7 months ago
genya35 ▴ 40

Hello, I would like to convert an unmapped bam to two fastq files and preserve RX tag that contains UMI information. Here is a bam tag example: A00839:75:HUHSSXY:2:1101:10004:29403 77 * 0 0 * * 0 0 ATCATATTATGAGCTTGATTCTTCAACCGTCACTCCATTTGGTAGTCAGGGAGAAAGTAAGTGTAGCTGCAAGGGGAAATGGAAAGAACTACCCTGCCCTTCTGCACCCCCAGCCAGGCCCACTAGCTGCGGTGCTGTGCACA FFF FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF ZA:Z:CTGGGTGT ZB:Z:AGAGAGGA RG:Z:A RX:Z:CTGGGTGT-AGAGAGGA

I've tried java -Xmx2g -jar /mctp/share/users/yelekley/scripts/picard.jar SamToFastq but the resulting fastqs don't seem to retain the tag. Resulting fastq example :

@A00839:75:HUHSSXY:2:1101:10004:29403/1
ATCATATTATGAGCTTGATTCTTCAACCGTCACTCCATTTGGTAGTCAGGGAGAAAGTAAGTGTAGCTGCAAGGGGAAATGGAAAGAACTACCCTGCCCTTCTGCACCCCCAGCCAGGCCCACTAGCTGCGGTGCTGTGCACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Any suggestions? I need the tag for the downstream analysis. Thanks

GATK • 231 views
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This tag is not part of the fastq format. Maybe here we need after you generate the fastq from the unmapped bam, you have to do that in shell maybe to append this information.

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