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Old 09-11-2015, 12:00 PM   #1
aprice67
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Location: New York

Join Date: Nov 2012
Posts: 49
Question Why isn't corset giving me output?

Hi,

I am a Ph.D student and this is my first time doing a differential expression study. I am having an issue with corset and was wondering if anyone here might be able to offer some guidance.

I have some bacterial RNA-seq reads and a reference genome from NCBI. I ran bowtie2 to align the reads and made a .sam file, which I then converted to a .bam file using samtools. I did this for two different experiments that I want to do differential expression analysis on. I ran corset using the following command:

Quote:
corset -g 1,2 -n HS,ASW /projects/boom/data/CMCP6/reference/CMCP6_reference_HS_aligned_reads.bam /projects/boom/data/CMCP6/reference/CMCP6_reference_ASW_aligned_reads.bam
So the output looked fine for a while, it started with:
Quote:
Setting sample groups:1,2, 2 groups in total
Setting sample names to:HS,ASW
Reading bam file : /projects/boom/data/CMCP6/reference/CMCP6_reference_HS_aligned_reads.bam
0 million alignments read
0.2 million alignments read
0.4 million alignments read
. . . . .
and later continued to read the second file...

Quote:
Done reading /projects/boom/data/CMCP6/reference/CMCP6_reference_HS_aligned_reads.bam
Reading bam file : /projects/boom/data/CMCP6/reference/CMCP6_reference_ASW_aligned_reads.bam
0 million alignments read
0.2 million alignments read
0.4 million alignments read
0.6 million alignments read
0.8 million alignments read
1 million alignments read
1.2 million alignments read
But then at the end it gave me this:
Quote:
Done reading /projects/boom/data/CMCP6/reference/CMCP6_reference_ASW_aligned_reads.bam
Done reading all files.
Start to cluster the reads
0 million compact reads read
Starting hierarchial clustering...
0 thousand clusters done
Finished
There are no clusters.txt or counts.txt files, just this. I have no idea why. Also, I tried running HTSeq on the same stuff and just got 0 counts for every feature.

Can anyone offer me some guidance about what might be happening here?
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cluster, corset, differential expression, expression

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