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Old 07-28-2011, 01:23 AM   #1
fpauler
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Location: Vienna

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Default Multi-read problem with bowtie and cufflinks

Hi,

I am trying to use the sorted BAM files (samtools) from bowtie alignments with cuffdiff.

Although I allow bowtie to report multiple matching reads cuffdiff reports:
Multi-Reads: 0

The same cuffdiff parameters used for a TopHat alignment of the same data does show Multi-Reads!

Any ideas what could be the problem?

Thanks a lot!
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Old 02-11-2012, 12:31 PM   #2
chlamy18
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Default Did you find the solution.

I had the same problem as you posted last year on this forum.
I wonder if you found the solution how to deal with the multi-read in bam file generated by Bowtie.
Thanks.
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Old 02-15-2012, 12:19 AM   #3
fpauler
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Default

There seem to be some people interested as this post has 434 views but no replies.

So I investigated the matter and found the following:
Cuffdiff needs a certain nomenclature for multi-reads in the BAM file. This nomenclature is non-standard (at least for bowtie alone) but done by TopHat automatically. What TopHat basically does is to connect the multireads and make the analysis for cufflinks easier.

At the moment I use TopHat with a GTF file for my reference transcripts and use this output for cufflinks. This is quite quick and does the job.

I wished the tuxedo-suite developers cared more for their users and give this information somewhere ...

hope this helps,
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Old 02-15-2012, 12:46 PM   #4
chlamy18
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Default Thanks~

Thank you very much for the information.
Recently launched Bowtie2 generates much sensitive alignment compared to the previous Bowtie. So, I tried to avoid using Tophat because it still uses old Bowtie for its process.
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