User: oakhamwolf

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oakhamwolf20
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Posts by oakhamwolf

<prev • 12 results • page 1 of 2 • next >
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Comment: C: RNASeq - How to compare the expression of a single gene across batches
... Thank you for your reply. It is very much appreciated. I think I understand what you mean. Just so I have it straight.... 1. RE: Batch correction. When you say "it makes the average for each batch the same as the average for all other batches". Does that "average" refer to the average expression ...
written 8 days ago by oakhamwolf20
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Answer: A: looking for a way to identify a specific gene, and in varying numbers across mul
... If you have access to the genomic sequences of the isolate, could you just make a BLAST database out of them and search for your sequence that way? ...
written 8 days ago by oakhamwolf20
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RNASeq - How to compare the expression of a single gene across batches
... Hoping someone can help. Thanks for taking the time to read this post. I have RNA-Seq data from 7 different experiments (same assay type, just performed on a different day with different samples). I would like to compare the expression of a single gene across these samples. The read data has been a ...
batch correction rna-seq edger written 8 days ago by oakhamwolf20 • updated 8 days ago by i.sudbery9.4k
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Comment: C: edgeR analysis. Is my design matrix correct?
... Similarly, apologies for missing your response too. Many thanks. ...
written 13 days ago by oakhamwolf20
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Comment: C: edgeR analysis. Is my design matrix correct?
... My apologies for the late reply, I didn't receive any notifications of comments on my post and only just checked back into the forums. Consequently I missed your response. Many thanks. I've edited the post to include the code used to generate an MDS plot. Any help would be gratefully received. ...
written 13 days ago by oakhamwolf20
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Answer: A: how to add > to fasta file header and merge two line headers into one line(see b
... Assuming that your file has a consistent structure of ID #new line# Genus species #new line# sequence #new line# then the following will work: cat test | paste - - - - - - | awk -F "\t" -v OFS="\n" '{print ">"$1" "$3,$5;}' If you don't have the #new line# lines in ...
written 14 days ago by oakhamwolf20 • updated 14 days ago by RamRS30k
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Comment: C: Any problem re-using last year's RNA-Seq data in this year's analysis?
... ...also, how do I accept your comments as an Answer? ...
written 10 weeks ago by oakhamwolf20
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Comment: C: Any problem re-using last year's RNA-Seq data in this year's analysis?
... Great, thanks again. I agree about the good experimental design principles comment, this is mainly a stab at getting more sequencing data for our patient samples! So maybe the way forward would be, as you say, to not simply blindly use both control samples in the same analysis, but compare the patie ...
written 10 weeks ago by oakhamwolf20
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Comment: C: Any problem re-using last year's RNA-Seq data in this year's analysis?
... Thanks Joe, this is what my gut was telling me. Last year's data and this year's data are from iPSC-derived RPE cells, either from a control individual or from patients. I was mainly wondering whether the field had come far enough that current batch correction methods would allow me to incorporate l ...
written 10 weeks ago by oakhamwolf20
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Any problem re-using last year's RNA-Seq data in this year's analysis?
... Dear all, This may be a crazy simple question but one I am not sure about. Last year we did some RNA-Seq to identify any off-target effects for a therapeutic. This was a fairly simple experimental design involving three pseudo-biological replicates of an untreated control and two treatment doses. ...
"batch effect" rna-seq written 10 weeks ago by oakhamwolf20

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Scholar 14 days ago, created an answer that has been accepted. For A: how to add > to fasta file header and merge two line headers into one line(see b

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