User: abass.conteh

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Posts by abass.conteh

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Select what conditionsto graph in Report tools with Deseq containing multiple conditions
... Hello, I have been trying to setup a HTML report of DESEQ2 analysis using ReportingTools and have encountered some snags. My DESEQ2 analysis has 5 conditions and I want to create a report for each contrast. After reading some posts on this site I was able to get that to happen. Basically I can get ...
reportingtools deseq2 ggplot2 written 3.0 years ago by abass.conteh0
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Comment: C: SystemPipeR: alignments with ambiguous pairing were dumped.
... Thank you so much for the quick reply! I saw the error in the f() function after I posted it on here. That one line was the reason it kept failing, and after I had removed it, everything worked perfectly.  As for the alignments rate, I am not familiar with what is considered acceptable. So basically ...
written 3.0 years ago by abass.conteh0
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SystemPipeR: alignments with ambiguous pairing were dumped.
... Hello, I have some mouse RNA seq data I am trying to process and so far its been one issue after another. I am using SystemPipeR to complete the workflow. Most processes are done  on a school computer cluster Alignment with Tophat2 & Bowtie2  will not give me alignment percentage greater than ...
rnaseq R systempiper summarizeoverlaps tophat written 3.0 years ago by abass.conteh0 • updated 3.0 years ago by Thomas Girke1.7k

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