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Recent Replies
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
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?
by
benformatics
3.9k
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
★
5.8k
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.
https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis
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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
Comment: PCA plot
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ATpoint
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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…
Comment: genome assembly records not present in assembly_summary.txt
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Joe
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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 …
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J
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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
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> using bcftools
Show us what you tried
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> Hi, guys, there is a question about the genomic gVCF file. I wonder
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Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
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