anyone help me on bowtie format -> sam format!

[tninja]

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

[tninja]

solved

wrote some script to do that myself...

[baby1885]

You can try 'bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam',the -S option will make output file of sam format.