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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