Convert .Map To .Bam

How can i convert .map files generated from bowtie to .bam files using samtools?

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updated 14.3 years ago by dli

• written 14.3 years ago by ftp

Did you look at the bowtie tutorial ? http://bowtie-bio.sourceforge.net/tutorial.shtml

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written 14.3 years ago by jvijai

1 answer

There is bowtie2sam.pl script in samtools package, which you can used to convert your .map to .sam

$ ./bowtie2sam.pl 
Usage: bowtie2sam.pl <aln.bowtie>

then use samtools to convert .sam to .bam

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written 14.3 years ago by dli

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