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  • 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:

    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:
    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...

    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:
    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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