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Recent Replies
Answer: how to sort a fasta file
by
Jesse
▴
560
With [seqmagick](https://github.com/fhcrc/seqmagick):
```
seqmagick convert --sort name-asc file.fa file_sorted.fa
```
(Or `seqmagi…
Answer: BioInformatics, Software
by
Jesse
▴
560
Here's a couple that are geared toward hands-on bioinformatics learning:
* [rosalind.info](https://rosalind.info)
* [sandbox.bio](htt…
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Jeremy Leipzig
21k
> So how GATK called this ref allele if there is no reads supporting it
it didn't call it reference. it called it hom_alt. where in your f…
Comment: mutational signatures in different tumor samples
by
Vincent Laufer
★
2.9k
as far as im concerned, thats a recommendation not a disclaimer
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★
2.9k
Actually, I just remembered the perfect paper to illustrate that idea. Look at this: https://pubmed.ncbi.nlm.nih.gov/35976223/. In this man…
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★
2.9k
yep! updated my answer to respond to this. i think they ARE biological variables. it is understanding the nature of those variables that is…
Answer: ggsave() bug in ggplot2?
by
Medeea
•
0
I think the issue is solved with saving the file as .png
There must be a problem with the .jpg format then.
Thanks everyone for the va…
Comment: ggsave() bug in ggplot2?
by
Ram
39k
Try PDF. You won't need dpi for that. Also, do things work well if you use the lower level `png(); ggplot(); dev.off();` sequence instead o…
Comment: How to calculate kinship matrix table from vcf file
by
chrchang523
10k
The last vcftools release was in 2018. It has been superseded by bcftools for most purposes, and by plink 1.9/2.0 for most analytical func…
Comment: NarrowPeak format -Peak field
by
ATpoint
72k
I do not follow, can you please add a chr-start-end example.
Comment: BioPython: convert fasta to fastq without quality score input file
by
capemaster
•
0
The command with `gawk` is:
awk 'BEGIN {RS = ">" ; FS = "\n"} NR > 1 {print $1"\n"$2"\n+\n"gensub(/./, "I", "g", $2)}'
Comment: The inchworm process failed. Trinity running error.
by
GenoMax
129k
So with 600M reads you will need a minimum of 600GB of RAM per trinity recommendations.
If you are not able to get more memory consider no…
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
I don't understand what you're saying. Your allele is different from the ref allele so it needs the sample to support that? Why?
Give me t…
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