Brandon,

These type of questions--questions about to use Galaxy--are best directed to
the galaxy-user list, so I've moved it there.


> I saw this thread, though it is older I just want to make sure I did my
> analysis after the update.
>
> http://www.mail-archive.com/galaxy-user@lists.bx.psu.edu/msg00084.html
>
> You mention having to repeatedly merge cufflinks output for cuffcompare to
> generate the combined transcripts.  I was able to add them all in the
> cuffcompare section with the "add new Additional GTF input file". also my
> command is:
>
>
>
> cuffcompare -o cc_output -r
> /galaxy/main_database/files/002/048/dataset_2048606.dat -R -s
> /galaxy/data/hg19/sam_index/hg19.fa ./input1 ./input2 ./input3 ./input4
> ./input5 ./input6 ./input7 ./input8 ./input9 ./input10
>

This is correct: Galaxy now supports an arbitrary number of input files to
cuffcompare, making repeated merging unnecessary.


> Also I was reading on seqanswers that cuffdiff didn't work with biological
> replicates
>
> http://seqanswers.com/forums/archive/index.php/t-7905.html, but when I did
> my galaxy analysis it had the "perform replicate analysis" available and was
> wondering if you had an updated version or did something else. I am
> analyzing a control and diseased group, with 5 biological samples in each
> group.  Cuffdiff should work fine on this right?  I got FPKM as output.
> Also do you know what statistical methods cuffdiff is using for analysis?
>

Cuffdiff claims to support biological replicates, and, as you found, Galaxy
provides the infrastructure to specify replicates to Cuffdiff. I do not know
the statistical methods used for analysis, but this would be a good question
to ask either on seqanswers or on the new tophat-cufflinks mailing list:
tophat.cuffli...@gmail.com


> Lastly, in cuffdiff, the CDS, promoters and splicing analyses didn't seem
> to work (datasets 190,191,192).  any ideas?
>

This is because the p_id attribute is not being attached to the
combined_transcripts dataset produced by Cuffcompare. This problem is due to
your reference file being incorrect -- it should be dataset 81, your
reference annotation.

Thanks,
J.
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