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
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genya35 •
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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.