Hi Mete,

I am not sure it is the "sort" problem. I find "cufflinks" in galaxy is
unstable. I have bam files from Tophat which I can run cufflinks a few days
agao.

But these days when I run cufflinks with these bam files, the error shows.
Strangely, it can work some time. I don't know the reason.

ChenYao

2011/8/9 Jennifer Jackson <j...@bx.psu.edu>

> Hi Mete,
>
> This FAQ has a workflow for sorting a Bowtie (or any) SAM file for
> Cufflinks:
> http://main.g2.bx.psu.edu/u/**jeremy/p/transcriptome-**analysis-faq#faq2<http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2>
>
> Thanks!
>
> Jen
> Galaxy team
>
>
> On 8/4/11 10:27 AM, Mete Civelek wrote:
>
>> Hi,
>>
>> I'm trying to get read counts or FPKM values for my miRNA NGS data on
>> Galaxy. I have aligned the reads using Bowtie, but it appears that
>> Cufflinks gives an error when run on the Bowtie alignments (This might
>> have something to do with Bowtie's BAM file not being sorted). I know
>> that Tophat alignments work well with Cufflinks, but I'm not sure if it
>> would be possible to use Tophat for my data since miRNA don't have
>> splice junctions. I've tried without success to parameterize Tophat to
>> completely avoid assigning splice junctions (by setting the max intron
>> length to 1). Is there a way I can get the Bowtie alignment to work with
>> Cufflinks on Galaxy? Or perhaps there's a way I can parametrize Tophat
>> as to get no splice junctions?
>>
>> Thanks,
>>
>> Mete
>>
>>
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