Hello, I am running the following pipeline:
tophat -p 4 -G genes.gtf -o sample1TopHat genome sample1R1.fastq sample1R2.fastq
tophat -p 4 -G genes.gtf -o sample2TopHat genome sample2R1.fastq sample2R2.fastq
cufflinks -o sample1Cufflinks -p 4 -G genes.gtf sample1TopHat/accepted_hits.bam
cufflinks -o sample1Cufflinks -p 4 -G genes.gtf sample1TopHat/accepted_hits.bam
cuffmerge -o sampleCuffMerge -p 8 -g genes.gtf -s genome.fa assemblylist.txt
cuffdiff -o sampleCuffdiff -p 8 -b genome.fa -L s1,s2 -u sampleCuffMerge/merged.gtf sample1TopHat/accepted_hits.bam sample2TopHat/accepted_hits.bam
However, I am getting NOTEST on the splicing.diff, whereas the isoform_exp.diff does show some information. I am just not sure how to debug this. Any suggestions?
I have messed with the -c flag in cuffdiff. I am using cufflinks 2.2.1, and I am using the UCSC Homo Sapiens HG19 genome and annotation (genes.gtf). Any suggestions appreciated.
Thank you in advance,
Ramiro
tophat -p 4 -G genes.gtf -o sample1TopHat genome sample1R1.fastq sample1R2.fastq
tophat -p 4 -G genes.gtf -o sample2TopHat genome sample2R1.fastq sample2R2.fastq
cufflinks -o sample1Cufflinks -p 4 -G genes.gtf sample1TopHat/accepted_hits.bam
cufflinks -o sample1Cufflinks -p 4 -G genes.gtf sample1TopHat/accepted_hits.bam
cuffmerge -o sampleCuffMerge -p 8 -g genes.gtf -s genome.fa assemblylist.txt
cuffdiff -o sampleCuffdiff -p 8 -b genome.fa -L s1,s2 -u sampleCuffMerge/merged.gtf sample1TopHat/accepted_hits.bam sample2TopHat/accepted_hits.bam
However, I am getting NOTEST on the splicing.diff, whereas the isoform_exp.diff does show some information. I am just not sure how to debug this. Any suggestions?
I have messed with the -c flag in cuffdiff. I am using cufflinks 2.2.1, and I am using the UCSC Homo Sapiens HG19 genome and annotation (genes.gtf). Any suggestions appreciated.
Thank you in advance,
Ramiro
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