Hi,
We are running tophat/cufflinks on 3 identical human rna samples which were sequenced in 3 different lanes on 2 different flowcells. All 3 samples are from the exact same library.
When running cufflinks, the genes.fpkm_tracking file for one sample is showing some genes with 0 FPKM and status FAIL, however these same genes in the other two samples are showing a non-zero FPKM.
We are using tophat-1.4.0, bowtie-0.12.7, and cufflinks-1.3.0
We ran tophat with the -G option and provided the gtf file. We ran cufflinks with -G option providing the same gtf file that we gave to tophat. We also ran cufflinks with -u -N --compatible-hits-norm -b hg19_ucsc.fa
We've tried running without options -N and --compatible-hits-norm but still had the same results.
We are confused how with 3 identical samples, one shows up with 0 FPKM but the other two seem to have valid FPKM's. For the 0-FPKM gene, we checked the bam file in IGV and it is definitely mapped.
Has anyone encountered a similar problem or does anyone have any insight into this?
Thanks!
--Jennifer
We are running tophat/cufflinks on 3 identical human rna samples which were sequenced in 3 different lanes on 2 different flowcells. All 3 samples are from the exact same library.
When running cufflinks, the genes.fpkm_tracking file for one sample is showing some genes with 0 FPKM and status FAIL, however these same genes in the other two samples are showing a non-zero FPKM.
We are using tophat-1.4.0, bowtie-0.12.7, and cufflinks-1.3.0
We ran tophat with the -G option and provided the gtf file. We ran cufflinks with -G option providing the same gtf file that we gave to tophat. We also ran cufflinks with -u -N --compatible-hits-norm -b hg19_ucsc.fa
We've tried running without options -N and --compatible-hits-norm but still had the same results.
We are confused how with 3 identical samples, one shows up with 0 FPKM but the other two seem to have valid FPKM's. For the 0-FPKM gene, we checked the bam file in IGV and it is definitely mapped.
Has anyone encountered a similar problem or does anyone have any insight into this?
Thanks!
--Jennifer
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