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updated 24 days ago by
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written 15 months ago by
javanokendo
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updated 7 days ago by
joe
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written 9 days ago by
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15 days ago by
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9 days ago by
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updated 3 days ago by
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written 6.1 years ago by
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BioinfGuru
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written 18 days ago by
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updated 5 days ago by
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written 8 days ago by
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updated 8 days ago by
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written 5.1 years ago by
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10 days ago by
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updated 8 days ago by
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written 4.8 years ago by
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written 3.8 years ago by
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Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★
3.8k
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
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Patadu94
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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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Patadu94
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For doing this, should I just look at the log.out.file?
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by
pinheirofabiano
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install.packages("pheatmap")
library(pheatmap)
setwd("/Users/data_analysis/results")
data <- read.table(file…
Comment: Low mapping rate with Salmon
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Patadu94
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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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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…
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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…
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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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Can you clarify what `metainfo` you are referring to?
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Specifically:
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Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
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This is way easier to do solely in R now 10 years later.
library(GenomicFeatures)
library(rtracklayer)
## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
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I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
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The updated code in R using rtracklayer for reading a gtf file.
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Thank you LauferVA,
Your advice has been useful and I now a lot to think about and read.
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