Hi all.
I hope someone can help me with my cuffdiff problem, which I have been trying to work around for a few days now.
I guess I should mention that I am a novice at this...
I run cuffdiff on the output from Tophat like this:
But for some reason cuffdiff reports zero total map mass and read type as 0bp single-end
And the output files (like gene_exp.diff) just have zero for all values and fold changes
I also tried using bam files from a direct Bowtie alignment with the same results.
Software versions I am using:
Bowtie v 0.12.5
Samtools v 0.1.16 (r963:234)
TopHat v1.3.1 (also tried v1.2)
Cufflinks v1.0.3
I really hope someone can help me because I am completely stuck!
Thank you.
-Morten
I hope someone can help me with my cuffdiff problem, which I have been trying to work around for a few days now.
I guess I should mention that I am a novice at this...
I run cuffdiff on the output from Tophat like this:
Code:
cuffdiff -o ./cuffdiff -p 7 /media/bigdrive/morten/software/cufflinks-1.0.3.Linux_x86_64/Homo_sapiens_annotation_hg19-GRCh37.62.gtf T4A_1_L1-tophat/accepted_hits.bam T4C_1_L1-tophat/accepted_hits.bam
Code:
You are using Cufflinks v1.0.3, which is the most recent release. [10:51:59] Loading reference annotation. [10:52:07] Inspecting maps and determining fragment length distributions. Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided. > Map Properties: > Total Map Mass: 0.00 > Read Type: 0bp single-end > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided. > Map Properties: > Total Map Mass: 0.00 > Read Type: 0bp single-end > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 [10:53:16] Modeling fragment count overdispersion. Warning: compparcomp: perfect fit [10:53:16] Testing for differential expression and regulation in locus. > Processed 33455 loci. [*************************] 100% Performed 0 isoform-level transcription difference tests Performed 0 tss-level transcription difference tests Performed 0 gene-level transcription difference tests Performed 0 CDS-level transcription difference tests Performed 0 splicing tests Performed 0 promoter preference tests Performing 0 relative CDS output tests Writing isoform-level FPKM tracking Writing TSS group-level FPKM tracking Writing gene-level FPKM tracking Writing CDS-level FPKM tracking
I also tried using bam files from a direct Bowtie alignment with the same results.
Software versions I am using:
Bowtie v 0.12.5
Samtools v 0.1.16 (r963:234)
TopHat v1.3.1 (also tried v1.2)
Cufflinks v1.0.3
I really hope someone can help me because I am completely stuck!
Thank you.
-Morten
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