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04-25-2010, 12:27 PM
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#1 |
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Junior Member
Location: rockville, MD Join Date: Apr 2010
Posts: 2
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anyone help me on bowtie format -> sam format!
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 |
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04-25-2010, 01:53 PM
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#2 |
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Junior Member
Location: rockville, MD Join Date: Apr 2010
Posts: 2
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solved
wrote some script to do that myself...
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04-25-2010, 10:33 PM
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#3 |
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Member
Location: china Join Date: Jan 2010
Posts: 13
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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.
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