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Recent Replies
Answer: Need help teasing out insertions and deletions with bcftools stats file.vcf > fi
by
Afif Elghraoui
•
0
Not in one step that I could find, but this works:
deletions:
```
bcftools view --types indels --include 'ILEN<0' file.vcf | bcftools …
Comment: How to add gene information below the BSmooth result ?
by
diqixiaoyaoer
▴
10
Thank you, sir. I have looked into your thesis. It's really great. I may have a try on Gviz if I don't have any idea about my question.
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
by
rackbersingh
•
0
Brilliant, thanks for the advice, i think after looking into what the community has said I have invested into learning the groovy language …
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
Juke34
7.7k
Change merge_loci to true
Comment: msigdbr returns the same genesets for mouse as in for human,
by
igor
13k
The addition of mouse-specific pathways to MSigDB is relatively recent. The package has not been updated to incorporate the latest version …
Answer: known-sites for Felis_catus_9.0 (GCA_000181335.4)
by
makarov
•
0
Thank you, I also found vcf files
https://ftp.ensembl.org/pub/release-109/variation/vcf/felis_catus/
Comment: Creating a loop to mark duplicates using Picard
by
Ram
38k
For someone new at shell scripts, you're doing really well at using shell variables and parameter expansion. Good going!
Comment: Creating a loop to mark duplicates using Picard
by
brandnewatthis
•
0
Sorry, I am very new at this and am just learning my way around these symbols! Thanks for the help :)
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
BioinfoBee
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0
its version 1.0.0. and installed using conda. How do I configure config.yaml file in such case?
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
Ram
38k
> Can I
Yes. Should you? Probably not. There must be better, statistically more robust ways of quantifying based on biological replicates.
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
by
GenoMax
127k
> I can't find the way using the man documentation of bcftools to get a
> .vcf from a sorted .bam file.
This should be all you need: https…
Comment: RNA-SEQ
by
Trivas
▴
630
You should be able to do `fasterq-dump <SRR number> -O output_folder`
Comment: RNA-SEQ
by
GenoMax
127k
If you are trying to re-create an analysis and if it used both SRA# then you will need to get both. If you are simply learning/testing then…
Comment: wrong quality plots in fastqc output
by
poecile.pal
▴
50
I understood why I got high percentage of duplication. The size of reference was about 150K bp, while I asked for 30M reads with length 151…
Comment: RNA-SEQ
by
ali
•
0
so if I just consider one of the SRR and use fastq-dump --splite -files , its okay ???
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