Cuffdiff input error

Question

[ljohanam]

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

[ljohanam]

Thank you!!

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

Answer 1

[Devon Ryan]

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".

[Ram]

@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.