i'm a little confused as to why cufflinks didn't output a coverage estimate in the gene level tracking file. does anyone know what the reason is for this, and how i can derive an estimate of gene level coverage from the cufflinks output files?
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Cufflinks coverage no output
I run Cufflinks with no coverage output. Have you got the answer yet? Let me know. Thanks, Justin -
Cufflinks coverage from Tophat
I think I figure it out. Use "--coverage-search" option at Tophat run. I am rerunning it now.Originally posted by zhangju View PostComment
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Did this work for you? I'm also failing to get any gene-level coverage information (though it does work at the isoform level), and I usually run my tophat with --no-novel-juncs, so I'm a little hesitant to turn on --coverage-search, but if that's what I have to do...Originally posted by zhangju View PostComment
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This is my command line
"tophat -p ${NUM_PROCS} -o $OUTPUT --coverage-search -G $GTF --transcriptome-index=$TRANSINDEX $BINDEX $READ1 $READ2 $Orphan"
It works for me.
Originally posted by rflrob View PostComment
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You would try a small subset data to test this command. I could not remember well. I check my most current command without "coverage-search", so "coverage-search" may not help. I am running Bacterial genome, so I am using isoform data as gene data. I did not set "no-novel-junc" on purpose, and it did not find new juncs by program.
Originally posted by zhangju View PostComment
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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
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