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Old 11-19-2013, 01:08 PM   #1
liweixie
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Default cuffmerge

what command is used to merge several gtf file for cuffmerge.
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Old 11-19-2013, 01:41 PM   #2
dpryan
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cuffmerge is the command, or did you mean to ask a different question?
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Old 11-19-2013, 08:22 PM   #3
liweixie
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Quote:
Originally Posted by dpryan View Post
cuffmerge is the command, or did you mean to ask a different question?
I am sorry. I mean, cuffmerge need a txt file to put all gtf file in it. My question is how to make the txt file with all gtf in it that can be read by cuffmerge command?
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Old 11-20-2013, 12:17 AM   #4
dpryan
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You can make that with any text editor (notepad, vi, emacs, etc.). I usually process everything using a bash script, so I just have a line that does an
Code:
echo "$sampleName/transcripts.gtf" >> assemblies.txt
after processing each sample.
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Old 04-04-2014, 01:34 AM   #5
zzta
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I use the ls command:

Code:
ls *suffix_that_all_sample_directories_have_in_common/transcripts.gtf > all_assemblies.txt

Last edited by zzta; 04-04-2014 at 01:37 AM.
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