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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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Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...Today, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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