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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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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
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