Moderator: Kevin Blighe
Kevin Blighe ♦ 26k
- Reputation:
- 25,610
- Status:
- Trusted
- Location:
- USA / Europe / Brazil
- Website:
- https://github.com/kev...
- Last seen:
- 5 hours ago
- Joined:
- 11 months, 3 weeks ago
- Email:
- k**********@outlook.com
Irish bioinformatician. Previously worked in USA, Italy, Malta, Brazil, UK, and Ireland.
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Developer / Maintainer of Bioconductor packages:
- EnhancedVolcano (submitted)
- https://github.com/kevinblighe/CorLevelPlot (dev)
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There are mountains in our way... but we climb a step every day...
Nella fantasia, io vedo un mondo giusto; Lì, tutti vivono in pace e in onestà; Io sogno d'anime che sono sempre libere...
Posts by Kevin Blighe
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... Oh! You have to use plink v1.9: https://www.cog-genomics.org/plink2
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written 5 hours ago by
Kevin Blighe ♦ 26k
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... Please reply to cpad via the `ADD COMMENT` button ...
written 6 hours ago by
Kevin Blighe ♦ 26k
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... Yes, you can proceed ...
written 12 hours ago by
Kevin Blighe ♦ 26k
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... I think that you need to do the following (assuming that you have separate VCF files):
1. rename the sample ID in each file to have the same ID (`bcftools
reheader`)
2. concatenate all and remove duplicates (essentially a UNION of all
variants in all files) (`bcftools concat VCF1.vcf.gz V ...
written 12 hours ago by
Kevin Blighe ♦ 26k
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... That command requires a lot of memory. For the TCGA breast cancer data (~1000 samples), it neither runs on my laptop with 16GB RAM. Do you have access to a supercompute cluster? ...
written 14 hours ago by
Kevin Blighe ♦ 26k
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... You will likely / hopefully receive a more in depth response on Cross Validated, which is more 'statistics'-aligned than we are.
The simplest type of association test just looks at allele tallies in cases versus controls and derives a Chi-square *P* value from this, as I go over step-by-step here: ...
written 15 hours ago by
Kevin Blighe ♦ 26k
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...
# BEDTools getfasta
You can use BEDTools getFasta:
cat test.bed
5 1000000 1000500
9 5000 6000
bedtools getfasta -fi 1000Genomes/human_g1k_v37.fasta -bed test.bed -fo test.fasta
cat test.fasta
>5:1000000-1000500
GTTTTAACTAAACTAACTCCCCAAAAACTGGACACGTGACTTC ...
written 15 hours ago by
Kevin Blighe ♦ 26k
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... Maybe try to increase the adjusted P value threshold from `threshold=0.15` to `threshold=0.2`?
What is the output of `head(cnv_obj)` ? ...
written 17 hours ago by
Kevin Blighe ♦ 26k
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... Do not worry, my friend. Perhaps you can contact the developers of the program: https://omictools.com/hlascan-tool
From what I can see, the program result is HLA-A, that is, the program identified that your sample sequence data contained HLA Class A. ...
written 1 day ago by
Kevin Blighe ♦ 26k
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... miqrom, you have never definitively explained what you want. Some test input and expected output would be a great help for both Ram and I. We are volunteers and are aiming to help you on our own free time. ...
written 1 day ago by
Kevin Blighe ♦ 26k
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