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Comment: Calculate RPKM
by
seidel
10k
You're welcome to contact me, but you should just ask the forum overall with a new question. You'll likely get much better answers.
Answer: How to implement this two-stage one-to-many workflow using WDL?
by
Geraldine
▴
10
I believe you’re looking for the scatter function. If you set the output of FIRST to be a list of files, you can simply set up a scatter() …
Comment: How can I determine the number of detected genes and detected transcripts/isofor
by
O.rka
▴
650
That's what I was expecting but I got the opposite where there were more detected genes relative to the number of detected transcripts. Ki…
Comment: How can I determine the number of detected genes and detected transcripts/isofor
by
GenoMax
126k
You have this tagged as single cell so assuming that is what the data is referring to perhaps you should have been using `STARsolo` or `ale…
Comment: How to perform synteny alignments and plots only with a gene?
by
cmdcolin
★
2.9k
if you want a 'genome browser' type approach, could try jbrowse 2, I am a developer of it. it has pairwise synteny visualization features l…
Comment: Calculate RPKM
by
Chris
▴
70
Thank you so much! I figured it out a few hours ago. Could I ask you questions about ATAC-seq?
Comment: Calculate RPKM
by
seidel
10k
the easiest way is to probably take the numeric columns of your data frame and create a matrix. For instance, if column 1 is gene names, an…
Comment: Processing fastqs generated by inDrop protocol
by
Ram
38k
You've [cross-posted this on bioinformatics SE][1]. Don't do that - a bunch of people are on both forums are it is bad etiquette to waste v…
Comment: How to adjust for multiple batches using Combat-Seq
by
Ram
38k
Even if the batches were meaningfully distributed, OP doesn't need to use ComBat-seq for batch especially when they're trying to do DE - th…
Comment: Processing fastqs generated by inDrop protocol
by
benformatics
3.5k
i'm just guessing but there is an 8 bp read and a 16 bp read so my guess is those are the non-transcriptomic part (maybe a UMI + cell barco…
Answer: How to adjust for multiple batches using Combat-Seq
by
ATpoint
70k
Cancer is nested with batch, meaning batch 4 and cancer is the same thing. There is nothing you can correct for. This analysis is not meani…
Comment: How can I determine the number of detected genes and detected transcripts/isofor
by
O.rka
▴
650
I probably should have used salmon in the first place but wanted to knock-out-2-bird-with-one-stone in creating a wrapper for STAR for anot…
Comment: Pig Reference Genome
by
Joe
20k
If you are not sure which file you need, are you sure you're equipped to analyse the data it spits out, or that you are even doing the corr…
Comment: How can I determine the number of detected genes and detected transcripts/isofor
by
GenoMax
126k
Looks like you have already used `featureCounts` which is what would be recommended here.
If you want to do transcript level estimations …
Comment: How to extract/find the actual names of the gene_IDs if they are not fully prese
by
GenoMax
126k
You could Convert your annotation file into Simple Annotation Format (SAF) that featureCounts understands. You will need to pull out `GENE_…
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