Multi-read problem with bowtie and cufflinks

[fpauler]

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!

[chlamy18]

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.

[fpauler]

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,

[chlamy18]

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.