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Search: Posts Made By: staylor
Forum: Bioinformatics 12-08-2009, 02:08 PM
Replies: 7
Views: 4,318
Posted By staylor
Try filtering for hits only (simple way is grep...

Try filtering for hits only (simple way is grep for chr if your genome uses this in the fasta header line) and then sort.
Forum: Bioinformatics 12-08-2009, 11:22 AM
Replies: 7
Views: 4,318
Posted By staylor
I did cuffcompare -r geneannotations.gtf...

I did

cuffcompare -r geneannotations.gtf 123.transcripts.gtf 456.transcripts.gtf

and got:

- - q1:CUFF.49|CUFF.49.0|100|320.741503|0.000000|0.000000|uniq -
- ...
Forum: Bioinformatics 12-08-2009, 09:17 AM
Replies: 7
Views: 4,318
Posted By staylor
:-) No problem. Thanks for your help.

:-) No problem.

Thanks for your help.
Forum: Bioinformatics 12-08-2009, 09:08 AM
Replies: 7
Views: 4,318
Posted By staylor
Do you mean I need to do cuffcompare -r...

Do you mean I need to do

cuffcompare -r geneannotations.gtf 123.transcripts.gtf 456.transcripts.gtf

otherwise how will the tracking file know about the two samples?



Ok. Thanks for your...
Forum: Bioinformatics 12-08-2009, 07:50 AM
Replies: 7
Views: 4,318
Posted By staylor
Tophat/cufflinks workflow question

If I have 6 samples, call them 1,2,3,4,5,6 (they could be 6 lanes or a 6 way multiplexed experiement). Then I want to compare 1,2,3 vs 4,5,6.

So if I map the reads using tophat, I assume I can run...
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