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Old 04-05-2012, 07:28 PM   #1
crh
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Location: tx

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Default cuffdiff Error: cannot open reference GTF file L for reading

Hi

I ran tophat with replicate samples for a control & treated sample, then ran cufflinks, followed by cuffmerge. I provided a GTF file to cuffmerge.

When I attempt to run cuffdiff I get the following error:
You are using Cufflinks v1.3.0, which is the most recent release.
Error: cannot open reference GTF file L for reading


my command line is:
cuffdiff -o diff_out -b genome.fa L C,T -u merged_asm/merged.gtf ./C1/accepted_hits.bam,./C2/accepted_hits.bam ./T1/accepted_hits.bam,./T2/accepted_hits.bam

Any suggestions?

thanks

Charles
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Old 04-07-2012, 04:06 AM   #2
mpiro
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the dash sign behind the L seems distorted .. I assume you copied the command from a web page .. please delete the -L and retype it.
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Old 04-08-2012, 01:50 PM   #3
crh
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Correct you are - retyping seems to have fixed the error - thanks!

Charles
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Old 03-28-2013, 12:07 AM   #4
Charitra
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Default

I have the same problem but after removing -L doesnt work.
my commands are:
cuffdiff -o diff_out -b genome.fa -p 8 calu,h358 -u merged.gtf, \ accepted_hits.bam accepted_hits1.bam
or
cuffdiff -o diff_out -b genome.fa -p 8 calu,h358 -u merged.gtf, \ ./accepted_hits.bam, accepted_hits1.bam

Error: cannot open reference GTF file merged.gtf, for reading

My both .bam files are in the same working directory but still the error ?
?????
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Old 04-14-2014, 02:52 PM   #5
jeales
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You do need the "-L" before your labels
But sometimes webpages, text editors and Word can insert non-standard hyphen-like characters like this "–", these then get copied and pasted in command lines and scripts and cufdiff etc have no idea what they are
Just type out the command fully yourself and use the proper hyphen button on your keyboard
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