Dear all,

I have a similar problem when using cufflinks in galaxy (net version). If I
didn't select the reference annotation, I can get the FPKM values,but since
no reference,I can not get the transcript or gene name. It looks like these:

test_id gene_id gene locus sample_1 sample_2 status value_1 value_2
ln(fold_change) test_stat p_value q_value significant
TCONS_00000002 XLOC_000025 - chr1:33860011-33860048 q1 q2 NOTEST 1.794e+06 0
-1.79769e+308 -1.79769e+308 0.0188163 1 no

There is no gene_id. However, if I use the reference annotation downloaded
from ENSEMBLE.I can get the gene_ids, but there FPKM values are all "0":

tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus
length coverage status FPKM FPKM_conf_lo FPKM_conf_hi
ENSMUSG00000024232 - - ENSMUSG00000024232 Bambi - 18:3507954-3516402 - - OK
0 0 0
ENSMUSG00000091539 - - ENSMUSG00000091539 Vmn1r238 - 18:3122454-3123465 - -
OK 0 0 0

------------------
Any thoughts?

2011/8/3 Jennifer Jackson <j...@bx.psu.edu>

> Hi Aleks,
>
> Thanks for sending the data link, this helped to narrow down the root cause
> of the issue.
>
> The UCSC-sourced GTF file has the attributes gene_id and transcript_id set
> to the same value (both as transcript_id). The result of this is that each
> transcript is interpreted by Cufflinks as a single gene, with no gene
> grouping (thus no isoforms).
>
> We have plans to develop a work-around. This would likely involve (for the
> refGene track in particular) the value in the UCSC's primary table
> refGene.name2 being swapped into the refGene GTF file's gene_id value. This
> would generate accurate gene-level statistics when the file is used as input
> to Cufflinks. You could do the same swap (outside of Galaxy) if you wanted
> to give it a try and have resource.
>
> Very sorry for the current inconvenience,
>
> Best,
>
> Jen
> Galaxy team
>
> On 7/25/11 11:26 AM, Jennifer Jackson wrote:
>
>> Hello Aleks,
>>
>> Chromosome names must be exact between all input files). Also, the SAM
>> file and GTF file both must be sorted the same way. This FAQ may be of
>> interest:
>> http://main.g2.bx.psu.edu/u/**jeremy/p/transcriptome-**analysis-faq<http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq>
>>
>> If still a problem, please share the history with me directly either
>> using my email address or generate the share link and email to me
>> (only). Use "Options -> Share or Publish", not just your sessions
>> browser URL.
>>
>> Best,
>>
>> Jen
>> Galaxy team
>>
>> On 7/22/11 8:45 AM, Aleks Schein wrote:
>>
>>>
>>> Dear all,
>>> I am trying to run Cufflinks installation in Galaxy on Solexa RNAseq
>>> samples from HeLa cells.
>>> Running Cuffcompare, according to the manual, should produce a tmap
>>> file, listing FMI values for detected isoforms. However, my files only
>>> have either "100" or "0" in FMI field. And FPKM column contains only
>>> zeros.
>>> Is there something wrong with my input files, or parameter settings? Or
>>> is it rather a specific issue with Galaxy Cufflink's installation?
>>>
>>> The data in question is available here:
>>> http://main.g2.bx.psu.edu/u/**aleks/h/guided-**assemblyadvanced<http://main.g2.bx.psu.edu/u/aleks/h/guided-assemblyadvanced>
>>>
>>> Thanks,
>>>
>>> Aleks Schein
>>>
>>>
>>>
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>>
>>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/**Support <http://galaxyproject.org/Support>
> ______________________________**_____________________________
> The Galaxy User list should be used for the discussion of
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>  
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