Error at flair collapse

[brookslabucsc]

Error at flair collapse

[csoulette]

Hi martynakgajos,

I can't see any noticeable errors in the way you've written out your commands, but it looks like FLAIR was expecting a file to exists that may not have actually been created. Can you confirm if there are any intermediate files that were created in your run? Namely, there should be two BED formatted files containing your reads that have had their splice sites corrected. One should contained a label "corrected" and the other should be labeled "inconsistent." Can you check for these and whether or not the files contain any read information?

-CMS

[martynakgajos]

Following files exist:
$base".corrected_all_corrected.psl"
$base".corrected_all_corrected.bed"
$base".corrected._all_inconsistent.bed", and they look good.
However, there is no file: $base".corrected._all_inconsistent.psl" - should it be created? No error message was created by previous commands.

Additional files created in the process:
$base.sam
$base.unsorted.bam
shortreads_junctions.bed
$base.bed12

[belgravia]

There isn't a psl made for the *_all_inconsistent.bed file. You're right in passing the corrected.psl to from flair-correct to flair-collapse. However it looks like flair-collapse is erroring at the very first step and can't open the corrected.psl that you're giving it, I'm guessing because of a bad path.

Just to make sure - is the file made from the correction step $base".corrected_all_corrected.psl" or $base".corrected._all_corrected.psl"?