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Recent Replies
Comment: BioInformatics, Software
by
barslmn
★
1.5k
https://bio.tools/ is a great website indexing software used in bioinformatics.
Comment: BioInformatics, Software
by
Pierre Lindenbaum
154k
This is just too broad. what did you find so far ?
Answer: How to calculate kinship matrix table from vcf file
by
barslmn
★
1.5k
You can use the vcftools relatedness2 module. Which implements the method describes in the paper: https://academic.oup.com/bioinformatics/a…
Answer: How to convert bed file to vcf?
by
Pierre Lindenbaum
154k
use AWK, change the header, body according to your needs...
awk 'BEGIN {printf("##fileformat=VCFv4.2\n##INFO=<ID=END,Number=1,Type=I…
Comment: Doubt - installing LncTar software
by
Jeremiah
•
0
It is the full result, there is only one lncRNA and one mRNA in Examp1, and the output file is just like web version reult
Comment: How to get a comperative result of 2 bed files?
by
Pierre Lindenbaum
154k
convert the bed to vcf and use truvari.
Comment: bioinformatic analysis protocol performed by CD Genomics
by
barslmn
★
1.5k
Mail their representative you talked with before or their support and ask them. There may not be a citable source. However, you can write t…
Comment: How to get a comperative result of 2 bed files?
by
herh
•
0
Actually, I am asked to use [truvari tool][1] but it works with vcf datasets. So, indeed I need a benchmarking measurement. One bed file is…
Comment: Building Dict File for GATK
by
dare_devil
★
3.1k
Make sure that you have installed GATK in your system.
Then follow the commands: For example, to generate `.dict` for `Homo_sapiens_assemb…
Comment: Precision-recall curve to compare metagenome classifiers to a gold standard - Is
by
sneha.d
•
0
Hi, I'm trying to construct a similar curve using Kraken2 and Bracken report files. I'm trying to use the sklearn.metrics.precision_recall_…
Comment: How to convert *.hic file to *.mcool file?
by
NikhilP
▴
20
Thanks I'll check that too.
Actually I found a way to add weight column in the converted mcool file by using cooler package.
Answer: What is NCBI Gene ID, where to find it and how to convert to entrez ID?
by
Pegasus
▴
90
Hi,
I am facing the exact issue, have u had luck to solve it ? If yes, please share here.
Thanks
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★
2.8k
whether or not you should conduct a pooled analysis or a stratified analysis depends upon the ratio of between-group variance to within-gro…
Answer: BAM creation - vg surject vs vg mpmap output
by
Rachel
•
0
From what I understand, there is indeed a difference. vg surject recomputes the alignment produced with the reference used to build the gra…
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