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Recent Replies
Comment: ScRNA data question
by
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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starswillfade
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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…
Comment: genome assembly records not present in assembly_summary.txt
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Can you clarify what `metainfo` you are referring to?
The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
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i.sudbery
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Specifically:
If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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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)
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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?
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The updated code in R using rtracklayer for reading a gtf file.
https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
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The_PyPanda
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Thank you LauferVA,
Your advice has been useful and I now a lot to think about and read.
Also, I just wanted to clarify I do not ha…
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You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
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What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
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If you have the accession numbers can you not use something like `eutils`?
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> Next, I tried using bedtools window
but in your original post you said
> tried finding the intersection of these bed files using bedto…
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Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
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0
Thank you for replying Pierre.
I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP
awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
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> using bcftools
Show us what you tried
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