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Old 06-20-2012, 12:27 AM   #1
waspboyz
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Default Cufflinks non-model organism, issues with -b, and false concatenation of genes

Hello,
I have been working with the "tuxedo" package for a little while now, and have started getting the nice results that I want, but I still have a few nagging issues.

One is that when I use the -b option, for multi-read correction in cuffdiff, I get a segmentation fault at differing stages of the run, and thus no result. If I do not use this option, I basically get no results, and the gene_exp.diff is basically full of NOTEST and LOWDATA entries.

This is only an issue for the newest (and unfortunately much better) annotation and assembly, as when I run the package with the older files, it works generally fine (also with the -b option).

Is there anything in the genome fasta or bowtie mapping files that I should look for in order to fix this problem? If anyone wants to take a look, I would be more than happy to send the files...

Another issue I have is that at some point some clearly distinct genes are merged into one cufflinks transcript, so that in the gene_exp.diff file, an entry in the "gene" column would look like: Nasvi2EG000144,Nasvi2EG000145,Nasvi2EG000147,Nasvi2EG000149,Nasvi2EG000151 It is clear to me that I am losing quite some differential expression information due to this issue, and was wondering if there was a way to avoid it....
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Old 06-20-2012, 02:31 AM   #2
glados
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Are you using the 2.0.1 or 2.0.0 version? These issues are supposed to be fixed in that latest version. Another thing, -b is not multi-read-correction, it is frag-bias-correct.
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Old 06-20-2012, 02:40 AM   #3
waspboyz
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Quote:
Originally Posted by glados View Post
Are you using the 2.0.1 or 2.0.0 version? These issues are supposed to be fixed in that latest version. Another thing, -b is not multi-read-correction, it is frag-bias-correct.
This was in 2.0.1, as well as in earlier versions.
Of course you are right about -b, I thought I had fixed it, but at least I got it right in the tags
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Old 06-20-2012, 07:01 AM   #4
glados
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Ok. Then I don't know. Hopefully someone else do.
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cuffdiff, cufflinks, fragment bias, fusions, non-model organism

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