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Forum: De novo discovery 05-26-2011, 07:54 AM
Replies: 2
Views: 2,168
Posted By Enrico Palazzo
I guess that this is nearly impossible. To...

I guess that this is nearly impossible. To compare transcripts, they must either have the same positions in case and control (for all exons of a transcript) or you need a kind of similarity measure...
Forum: Literature Watch 05-19-2011, 12:56 AM
Replies: 1
Views: 2,884
Posted By Enrico Palazzo
Hi, your sample data bases on hg18 and its'...

Hi,

your sample data bases on hg18 and its' annotations. Could you please describe how to prepare hg19 annotation files properly? Or: much better ;) Could you provide these files as a download?
...
Forum: Bioinformatics 04-18-2011, 06:49 AM
Replies: 3
Views: 2,500
Posted By Enrico Palazzo
Hi Zheng, I have got the same problem. Did...

Hi Zheng,

I have got the same problem. Did you hear sth. about this problem yet?

Regards,
Christian
Forum: SOLiD 01-21-2011, 01:15 AM
Replies: 40
Views: 12,348
Posted By Enrico Palazzo
Yes, release date is March/2011. Does anybody...

Yes, release date is March/2011. Does anybody know the new output format? I believe it is called XSV or something like this..
Forum: Bioinformatics 11-21-2010, 03:30 AM
Replies: 15
Views: 4,969
Posted By Enrico Palazzo
Hi, I had the same problem with cuffcompare. I...

Hi,
I had the same problem with cuffcompare. I think cuffcompare generates illegal symbols if the strand orientation is unknown. Do you have entries like "^@" in the 7th column?

I fixed it with:...
Forum: Bioinformatics 10-25-2010, 03:50 AM
Replies: 2
Views: 4,024
Posted By Enrico Palazzo
same problem

Hi,

did you find a reason for this error? I get the same error running

tophat -p 8 --output-dir output/26_1 genome/Homo
_sapiens.hg19/hg19 readfiles/s_100617_3_1.fastq
...
Forum: Bioinformatics 08-12-2010, 12:35 PM
Replies: 19
Views: 9,908
Posted By Enrico Palazzo
Thanks a lot. Unfortunately I did not save the...

Thanks a lot. Unfortunately I did not save the STDOUT and the only log file produced by SpliceMap contains:

####Total####alljunction##########
total: 0
ave: nan
1: 0 ...
Forum: Bioinformatics 08-12-2010, 04:31 AM
Replies: 19
Views: 9,908
Posted By Enrico Palazzo
Hi, I ran SpliceMap on 2*76bp paired end...

Hi,

I ran SpliceMap on 2*76bp paired end reads (Mouse) and it did not produce any splice junction. (the bed files are empty). I expected that the problem was connected to the problem Lix had, so I...
Forum: Bioinformatics 08-03-2010, 02:46 AM
Replies: 5
Views: 5,023
Posted By Enrico Palazzo
Hi J, I'm new to this field and this is just a...

Hi J,
I'm new to this field and this is just a guess:
I think you have to run cuffcompare on the two GTF files produced in step 2 and your reference annotation file:
cuffcompare -r...
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