Cuffdiff input error
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0
Entering edit mode
7.3 years ago
ljohanam ▴ 30

Hey!!

Somebody can say what's wrong with my command:

cuffdiff -L C1,C3,C7,C11 -N --FDR 0.05 -o desenvolvimento3 cpapaya.gtf \
    /BAM/C1/CONTROL/P03C1_accepted_hits.bam,/BAM/C1/CONTROL/P33C1_accepted_hits.bam,/BAM/C1/CONTROL/P08C1_accepted_hits.bam \ 
    /BAM/C3/CONTROL/P03C3_accepted_hits.bam,/BAM/C3/CONTROL/P08C3_accepted_hits.bam,/BAM/C3/CONTROL/P33C3_accepted_hits.bam \
    /BAM/C7/CONTROL/P03C7_accepted_hits.bam,/BAM/C7/CONTROL/P08C7_accepted_hits.bam,/BAM/C7/CONTROL/P33C7_accepted_hits.bam \
    /BAM/C11/CONTROL/P03C11_accepted_hits.bam,/BAM/C11/CONTROL/P08C11_accepted_hits.bam,/BAM/C11/CONTROL/P33C11_accepted_hits.bam

at the end cuffdiff report this error:

open: No such file or directory
Error: cannot open file /BAM/C1/CONTROL/P03C1_accepted_hits.bam for reading. Unrecognized file type

Thank you all

RNA-Seq cufflinks cuffdiff • 3.4k views
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1
Entering edit mode

Thank you!!

In effect the error was /BAM... instead ./BAM.. before every directory!! Now, it's work :)

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3
Entering edit mode
7.3 years ago

It's unlikely that you actually have a /BAM directory. I assume you actually mean "./BAM/C1/CONTROL/P03C1_accepted_hits.bam", or more simply "BAM/C1/CONTROL/P03C1_accepted_hits.bam".

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@ljohanam:

Explaining a minor part here: in UNIX, / is the root directory. /BAM/ is a directory named "BAM" under the root directory. ./ (note the period symbol) signifies current directory. ./BAM/ refers to a directory named "BAM" under the current working directory.

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