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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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BioinfGuru
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1.7k
Hi,
Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
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Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
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If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value.
https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
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sapuizait
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jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
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bk11
★
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I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
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> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes?
Reads are likely aligning in regions wh…
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the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
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I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
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For doing this, should I just look at the log.out.file?
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install.packages("pheatmap")
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Comment: Low mapping rate with Salmon
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Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
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bedtools intersect \
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Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
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The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
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starswillfade
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I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
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![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
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