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I have a bam file with Unique Molecular Identifiers (UMIs) for each read present on the RX tag ( such as RX:Z:TGAGAAGGG), as expected by picard and fgbio tools.

However, several other tools (such as UMI-tools) expect the UMIs to be present at the end of the read name, such as (NB501943:73:HK333BGXC:3:12402:20313:16437_TGAGAAGGG).

Does anyone know of a tool to do this? I have an awk solution which I'll self-answer with, but I don't know whether that is robust.

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  • $\begingroup$ Did you check UMI-tools, this is afaik exactly what it is doing? $\endgroup$
    – user3051
    Nov 22, 2020 at 11:11
  • $\begingroup$ @ATpoint, unless I'm incorrect, UMI-tools can't do this directly. umi_tools extract moves sequences from a position in the FASTA sequence onto the read name, but in this case the reads have been added to a tag via fgbio. $\endgroup$
    – SPPearce
    Nov 22, 2020 at 11:38

1 Answer 1

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My current solution is (awk is not a tool I'm very familiar with, so this may not be good awk code, there is presumably a way to get it to print the header lines unmodified.):

samtools view -H temp.sam > temp2.sam
samtools view temp.sam | 
awk '{OFS = "\t"} {for(i=1;i<=NF;i++)  if ($i ~ /^RX:Z:/) {$1=$1"_"$i; gsub("RX:Z:","",$1); print}}' >> temp2.sam

This seems to work when I test it, but I don't know if I'm missing anything.

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