Question: Can FASTQ header tags be added to SAM file output from bowtie2 ?
gravatar for manojkumar_bhosale
12 weeks ago by
manojkumar_bhosale70 wrote:

I am looking for functionality similar to bwa mem in bowtie2. BWA MEM provides option "-C" to copy fastq header meta-information/comments to SAM file. See below help text from BWA MEM

"-C Append append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (e.g. barcode) to the SAM output. Note that the FASTA/Q comment (the string after a space in the header line) must conform the SAM spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output."

Is there any similar option available with bowtie2 ?

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by manojkumar_bhosale70

It's important to mention which version of bowtie, hopefully you are referring to bowtie2.

ADD REPLYlink written 12 weeks ago by Amar630

Is there any way to do it with bowtie2?

ADD REPLYlink written 11 weeks ago by manojkumar_bhosale70
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