the tophat generate the bam file instead of sam files?

dingkai0564 · 11-10-2010, 07:33 PM

I have a question:

when i trying to use tophat (to alignment in order to generate the SAM file when can be loaded into the cufflinks.Why the output only gives me bam files in the default sub-directories? Is there any way to generate the SAM file? or i have used the wrong parameters? I am using tophat 1.1.0

Thanks!

krobison · 11-10-2010, 08:33 PM

bam to sam conversion is easy with samtools

Code:

samtools view -h myfile.bam > myfile.sam

In any case, the current version of cufflinks will accept BAM, but the online documentation doesn't seem to reflect that yet. But I just successfully ran a bunch with bam as input (successfully=cufflinks ran; I haven't looked at the output yet).

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11-10-2010, 07:33 PM	#1
dingkai0564 Member Location: lasvegas Join Date: Nov 2010 Posts: 10	the tophat generate the bam file instead of sam files? I have a question: when i trying to use tophat (to alignment in order to generate the SAM file when can be loaded into the cufflinks.Why the output only gives me bam files in the default sub-directories? Is there any way to generate the SAM file? or i have used the wrong parameters? I am using tophat 1.1.0 Thanks!

11-10-2010, 08:33 PM	#2
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	bam to sam conversion is easy with samtools Code: samtools view -h myfile.bam > myfile.sam In any case, the current version of cufflinks will accept BAM, but the online documentation doesn't seem to reflect that yet. But I just successfully ran a bunch with bam as input (successfully=cufflinks ran; I haven't looked at the output yet).