Can FASTQ header tags be added to SAM file output from bowtie2 ?

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4.5 years ago

manojkumar_bhosale ▴ 70

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 ?

bwa bowtie alignment sequencing next-gen • 1.2k views

ADD COMMENT • link 4.5 years ago by manojkumar_bhosale ▴ 70

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

ADD REPLY • link 4.5 years ago by Mark ★ 1.5k

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Is there any way to do it with bowtie2?

ADD REPLY • link 4.5 years ago by manojkumar_bhosale ▴ 70

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