Hi,
I am using bowtie2 output (which is sam format natively) to pipe into samtools as such:
but I am losing the headers when piping.
Is there a way to maintain the headers from bowtie to samtools during the pipe. I can't seem to find an option in samtools view that does this.
thanks
I am using bowtie2 output (which is sam format natively) to pipe into samtools as such:
Code:
bowtie2 <all the arguments> | samtools view -S -F 4 -b - | samtools sort - file.sorted
Is there a way to maintain the headers from bowtie to samtools during the pipe. I can't seem to find an option in samtools view that does this.
thanks
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