Hi all:
I have some bowtie aligned reads with bowtie default .map format and I need to transform them into .sam format. I tried bowtie2sam.pl in samtools/misc directory of samtools package but to my suppriseing the coverted .sam file has no head line and thus cannot be coverted to .bam format and do pileup work further.
Anyone have idea to covert bowtie format to sam format in a right way?
best
Kang Tu
postdoc in NIH
I have some bowtie aligned reads with bowtie default .map format and I need to transform them into .sam format. I tried bowtie2sam.pl in samtools/misc directory of samtools package but to my suppriseing the coverted .sam file has no head line and thus cannot be coverted to .bam format and do pileup work further.
Anyone have idea to covert bowtie format to sam format in a right way?
best
Kang Tu
postdoc in NIH
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