Recent Votes
Recent Locations •
All
VIB, Ghent, Belgium, just now
Italy, 3 minutes ago
Cambridge, MA, 4 minutes ago
United States, 5 minutes ago
Glasgow, Scotland, 5 minutes ago
Cambridge, MA, USA, 6 minutes ago
Germany, 9 minutes ago
Recent Awards •
All
Teacher to
finswimmer
15k
Popular Question to
Chvatil
▴
70
Scholar to
Devon Ryan
101k
Popular Question to
dare_devil
★
1.5k
Popular Question to
lakhujanivijay
5.6k
Popular Question to
Ian
5.8k
Popular Question to
CY
▴
640
Recent Replies
Comment: sliding windows over genome
by
cmdcolin
★
2.1k
it seems like a workflow might be `samtools faidx yourfile.fa; bedtools makewindows -w 1000 -g yourfile.fa.fai`
Comment: sliding windows over genome
by
cmdcolin
★
2.1k
>windows at the chromosome level
why is this not what you want, or, what other way would you want it to work?
Answer: Project ideas
by
jared.andrews07
★
13k
This question has been asked many times:
https://www.biostars.org/p/81207/
https://www.biostars.org/p/128683/
https://www.biostars.org/p…
Comment: How to rearrange fasta headers
by
JC
13k
thanks, that is more clear, you can do with:
$ echo "tr|D7RED9|D7RED9_9MYCO NidA3 (Fragment) OS=Mycobacterium sp. py145 OX=767442 GN=n…
Answer: sliding windows over genome
by
Alex Reynolds
34k
Assuming your reference genome is `hg38` (replace it with the key for your assembly of choice), you can use `bedops --chop` and `awk` prett…
Comment: Beginners bioinformatics project with machine learning?
by
Jeremy
▴
110
This looks good to me. I use R for machine learning, although I believe Python is more popular. I would check with the people on Kaggle t…
Comment: How to count mapping rates for ChIP-seq?
by
Istvan Albert
93k
It is the number of primary alignments divided by the number of reads.
Comment: How to rearrange fasta headers
by
cpad0112
20k
check if one of these two works:
$ awk -F "GN=| " '/^>/{print ">"$10};!/>/' test.fa
$ seqkit replace -p '.*GN=(\w+)\s.*' -r '$1' t…
Comment: How to rearrange fasta headers
by
v.berriosfarias
▴
50
Thanks for your reply, sorry if I didn't explain well, the issue is that I have 334 sequences that are under a single fasta file. Each sequ…
Comment: How to count mapping rates for ChIP-seq?
by
baijiangshan9726
•
0
I see, thanks so much! So how do you usually count the mapping rate?
Comment: Count number of times a value appear in correlation matrix
by
ali
•
0
The Fisher transformation is applied after so it has nothing to do with it ( my bad I mentioned it ). My concern is why and how is possible…
Answer: how to find coordinates of 5prime and 3prime utr from transcriptome data generat
by
i.sudbery
14k
As far as I am aware, none of the standard transcript assembly tools (cufflinks/stringtie etc) have the ability to annotate the open readin…
Answer: WGBS data presentation
by
debora.gisch
•
0
Your question is not clear for me. If the file extension is a bedgraph file you can plot and see tracks throughout the genome with tool ca…
Answer: How to determine percentage missing genotypes in VCF/BCF?
by
chrchang523
9.2k
`plink2 --vcf <filename> --genotyping-rate`
`plink2 --bcf <filename> --genotyping-rate`
Answer: How to determine percentage missing genotypes in VCF/BCF?
by
Eric
•
0
Here is a solution with bcftools version 1.15.1
1. Use the +fill-tags plugin to add an INFO field, FMISS, with the fraction of samples w…
Traffic: 2188 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6