User: nikelle.petrillo

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Posts by nikelle.petrillo

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Comment: C: using paired end and single end data in featurecounts
... Thanks James. Yes, the PE data was aligned as PE and the SE data was aligned as SE. I would like to create 1 count matrix made from all 4 .sam files using featureCounts. Are you saying to create a count matrix for the 3 .sam files (PE data, using PE mode in feautreCounts) and a separate count matrix ...
written 2.2 years ago by nikelle.petrillo0
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RNA STAR to DESeq2
... Hi all,  I aligned my PE reads using STAR and I used the GeneCounts option to get a count matrix. I would like to use this count matrix with DESeq2, however, I'm having trouble formatting STAR's gene count into a count matrix that is recognized and works with DESeq2. Does anyone have any tips/ideas ...
deseq2 star count matrix written 2.2 years ago by nikelle.petrillo0 • updated 2.2 years ago by James W. MacDonald51k
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using paired end and single end data in featurecounts
... Hi all,  I have 4 .sam files after aligning. 3 of the SAM files were created from PE data, and 1 SAM file was created from SE data. I want to use featurecounts to create a count matrix, however, should I be using paired end mode or single end mode?  Thanks for the help,  Nikelle  ...
rsubread featurecounts written 2.2 years ago by nikelle.petrillo0 • updated 2.2 years ago by James W. MacDonald51k

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For RNA STAR to DESeq2

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