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Old 08-03-2010, 07:44 AM   #1
glacierbird
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Default ^@ in .combined.gtf from cuffcompare v0.8.4

Hi,

after cufflinks generates tnp1/transcripts.gtf tmp2/transcripts.gtf (attached: tmp_gtf.zip)

I run cuffcompare (attachted: combined_gtf.zip) to generate a .combined.gtf from both of these .gtf files by

> cuffcompare -p 5 tmp1/transcripts.gtf tmp2/trascripts.gtf

> less stdout.combined.gtf
"stdout.combined.gtf" may be a binary file. See it anyway?

column 7, which should be "strand" from GTF, is presented by a weired "^@" character.

Currently, I replace this column by "." .

I am wondering if anybody met the same problem before. Maybe Cole can help to explain?!

tmp_gtf.zip

combined_gtf.zip
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Old 08-16-2010, 02:55 AM   #2
Uwe Appelt
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Default

Quote:
Originally Posted by glacierbird View Post
Hi,

after cufflinks generates tnp1/transcripts.gtf tmp2/transcripts.gtf (attached: tmp_gtf.zip)

I run cuffcompare (attachted: combined_gtf.zip) to generate a .combined.gtf from both of these .gtf files by

> cuffcompare -p 5 tmp1/transcripts.gtf tmp2/trascripts.gtf

> less stdout.combined.gtf
"stdout.combined.gtf" may be a binary file. See it anyway?

column 7, which should be "strand" from GTF, is presented by a weired "^@" character.

Currently, I replace this column by "." .

I am wondering if anybody met the same problem before. Maybe Cole can help to explain?!

Attachment 459

Attachment 460
This is most likely due to the status of the v0.8.4 (svn r1370, 16-Jul-2010). Cole has provided this snapshot prerelease to overcome the "duplicate gff id" errors introduced in v0.8.3 (discussed in http://seqanswers.com/forums/showpos...90&postcount=7).

Best,
Uwe
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Old 01-14-2011, 12:42 PM   #3
AbrahamB
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Default

I went back and forth about rehashing an old thread or starting a new one, so my apologies if this is against board etiquette.

I have been getting a similar error with Bowtie 0.12.7, TopHat 1.1.4, and Cufflinks 0.9.3. The strand column in the *combined.gtf file created by cuffcompare occasionally has a ^@ instead of a + or -. The most frustrating thing about it is that I'm unable to upload it to the UCSC browser.

glacierbird, if you're still listening, would you be able to tell me how you replaced all these characters? I've tried using sed, grep, regex in perl, vi, emacs, gedit, and a few OpenOffice programs.

Uwe, do you know if this problem was the result of this duplicate gff error and if it was supposed to be corrected in the latest versions?

Many thanks.
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