Can FASTQ header tags be added to SAM file output from bowtie2 ?
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 ?
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It's important to mention which version of bowtie, hopefully you are referring to bowtie2.
Is there any way to do it with bowtie2?