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Search: Posts Made By: Kcornelius
Forum: Bioinformatics 04-30-2012, 04:02 PM
Replies: 6
Views: 6,840
Posted By Kcornelius
Sure, I have posted one in a related thread:...

Sure,

I have posted one in a related thread:

http://seqanswers.com/forums/showthread.php?t=19533
Forum: Bioinformatics 04-30-2012, 08:38 AM
Replies: 6
Views: 6,840
Posted By Kcornelius
Hi Shen, when you use cuffmerge, do you see...

Hi Shen,

when you use cuffmerge, do you see any skipped regions with mouse?
Have you checked the transcript lengths of the new assembly?
I have seen in my output extremely long merged genes...
Forum: Bioinformatics 04-27-2012, 09:17 AM
Replies: 5
Views: 2,914
Posted By Kcornelius
Yes, we are disappointed by the results from...

Yes,
we are disappointed by the results from cuffmerge as well. Why nearly the whole chr21 gets pasted together is a mystery as nothing hints to this behaviour in the code description.
Working...
Forum: Bioinformatics 04-25-2012, 04:05 PM
Replies: 5
Views: 2,914
Posted By Kcornelius
Confirmed, merged.gtf did not contain the...

Confirmed,

merged.gtf did not contain the GeneIDs of the skipped region. So would be nice to get an idea if cuffmerge makes sense at all for human assemblies?
Forum: Bioinformatics 04-25-2012, 03:37 PM
Replies: 5
Views: 2,914
Posted By Kcornelius
Strange, I think I have no choice but to run...

Strange, I think I have no choice but to run cuttdiff with the reference gtf for now if I want to stick with the tuxedo pipeline. Need to run it again and test if all the known reference IDs of the...
Forum: Bioinformatics 04-25-2012, 12:51 PM
Replies: 5
Views: 2,914
Posted By Kcornelius
cufmerge and the max-bundle-length

Hi,

I could finally run cuffmerge but I realized that me and a colleague of mine got some
annoying skipping with human samples:

chr21:38435145-45760353 Warning: Skipping large bundle.
...
Forum: RNA Sequencing 04-25-2012, 09:14 AM
Replies: 9
Views: 9,024
Posted By Kcornelius
I am working on human as well. Me and a...

I am working on human as well.
Me and a colleague of mine got 2 regions bigger than 3.5 mio:

chr21:38435145-45760353 Warning: Skipping large bundle.

chr6:126102278-130463972 Warning:...
Forum: Bioinformatics 04-24-2012, 03:01 PM
Replies: 4
Views: 3,793
Posted By Kcornelius
Running now with the newer...

Running now with the newer Homo_sapiens.GRCh37.66.gtf and it is fine so far.
I guess my old reference file was somehow corrupted.
Forum: Bioinformatics 04-23-2012, 03:35 PM
Replies: 4
Views: 3,793
Posted By Kcornelius
ok, the cuttdiff part seems to run now for 2...

ok, the cuttdiff part seems to run now for 2 sets, one having a gtf with only chrX chrY and chrM. The sorting with one gtf file was done according to the header file I got for cuffmerge but is not...
Forum: Bioinformatics 04-23-2012, 11:02 AM
Replies: 4
Views: 3,793
Posted By Kcornelius
no luck with cuffdiff either

So, when using cuffdiff and say :

cuffdiff -N -o diff_out -p 1 -L C1,C2 -u Homo_sapiens.GRCh37.62.gtf ~/s_1_sequence_gtf_tophat_accepted_hits.bam ~/s_2_sequence_gtf_tophat_accepted_hits.bam

I...
Forum: Bioinformatics 04-23-2012, 09:45 AM
Replies: 4
Views: 3,793
Posted By Kcornelius
Cuffmerge error: loading reference annotation failed?

Hi,

I am trying to run cuffmerge for quite some time now but so far I always get the same message:


[Thu Apr 19 18:41:47 2012] Beginning transcriptome assembly merge...
Forum: Bioinformatics 04-18-2012, 09:12 AM
Replies: 7
Views: 2,172
Posted By Kcornelius
Smile Hi Simon, thanks a lot, I was not aware that...

Hi Simon,

thanks a lot, I was not aware that you could capture the next line with <> inside a while loop (but then every time you call <> it iterates to the next line, so I was not seeing the...
Forum: Bioinformatics 04-17-2012, 04:56 PM
Replies: 4
Views: 2,504
Posted By Kcornelius
same thing happens with Homo_sapiens.GRCh37.62.gtf

Hi,

I get the same error message and I used the Homo_sapiens.GRCh37.62.gtf
from ftp://ftp.ensembl.org/pub/release-62/gtf/homo_sapiens/

So, I need to provide chr1, chr2, etc in collumn 0...
Forum: Bioinformatics 04-17-2012, 01:19 PM
Replies: 7
Views: 2,172
Posted By Kcornelius
perl woes and the processing with big fatq files

Hi,
the last fastq files I got for an RNA-seq experiment had for some reason a glitch, that is
there was at least one field which was not starting with + like:...
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