User: nancy

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nancy30
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Posts by nancy

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Comment: C: 6-bp deletions in RNA-seq data
... "In short, the peak in 6-bp deletions is due to repetitive elements in the genome, and a single gene accounts for most of it. I am no longer worried. Thank you all for the input!!" Wonderful. Thanks so much for updating and sharing your code! p.s.: As an aside, it might be worth doing an overall ...
written 5 days ago by nancy30
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Answer: A: 6-bp deletions in RNA-seq data
... Hi Thomas, I don't exactly know how, but can point you in the direction: Once you align, you can extract deletion containing reads by parsing the CIGAR string in the bam file (http://felixfan.github.io/bam-sam/) Not sure you can specifically get at 6 bp long deletions, or just all reads with delet ...
written 9 days ago by nancy30
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Comment: A: 6-bp deletions in RNA-seq data
... Can you capture the deletion containing reads and visualize them in a a genome browser, to see the location? If its adapter related, it should be at the ends. In which case you can safely ignore. Would be really curious to know what you find :-) ...
written 12 days ago by nancy30
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What measure should be used to calculate fold-change while using Ballgown to compare D.E genes between 2 conditions?
... We would like to determine differentially expressed genes between two conditions. We are trying to use the Pertea et al pipeline (Hisat2+Stringtie+Ballgown). Following questions: 1. should the fold change be computed using the fpkm measure or any other? 2. If we use libadjust=FALSE, are the fold-c ...
ballgown stringtie rna-seq hisat2 written 5 weeks ago by nancy30
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stringtie + ballgown for multivariate analysis of rna-seq data
... I have RNA-seq data from 2 different genotypes, and each includes a treated versus mock-control. I'd like to use the hisat2+stringtie+ballgown pipeline to identify D.E. genes between the two genotypes, in treated vs control. I am unable to come up with the right stattest argument to code for this. ...
stringtie ballgown rna-seq multivariate written 4 months ago by nancy30

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Scholar 8 days ago, created an answer that has been accepted. For A: 6-bp deletions in RNA-seq data

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