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Recent Replies
Comment: What does ALT[0] mean?
by
Emms
•
0
thanks for reply. but I still don't understand. could you please explain in more detail?
Comment: Combining multiple 10x scRNAseq datasets
by
Alex Gibbs
▴
80
Can you reccommend, in your opinion, the best integration method that may be worth me looking into/trying?
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Carambakaracho
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Completely off topic, but in my experience once my program exceeded the available RAM and used swap it was as good as dead, so I usually do…
Comment: Mince a vcf into n bins of a given range
by
AndrMod
•
0
Thanks, this seems to work for the overall binning!
I just wonder if there is a way to recover the names of the SNPs stored in each bin.
Answer: What does ALT[0] mean?
by
Pierre Lindenbaum
141k
`ALT[0]` is the [first][1] ALTernate allele of the variant.
[1]: https://en.wikipedia.org/wiki/Zero-based_numbering
Comment: SNPid or chromosomal number and position in vcf
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https://www.biostars.org/p/86690/
Comment: PCA from gene count matrix with two conditions
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ATpoint
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`?plotPCA` and read the manual.
Comment: SNPid or chromosomal number and position in vcf
by
Nai
▴
20
I don't have this file rs #CHROM:POS which is related to my SNP.txt
Comment: SNPid or chromosomal number and position in vcf
by
Nai
▴
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I don't have this file
rs #CHROM:POS
Answer: Ubuntu 20.04 Crash
by
bala
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Thank you for your reply
My file size is 14 gb (paired shot-gun metagenome sample) and the reference database of 16.8 gb
Now i have inc…
Comment: SNPid or chromosomal number and position in vcf
by
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get a file `rs# CHROM:POS` and use `join` to merge both files. https://linuxconfig.org/join
Comment: PCA from gene count matrix with two conditions
by
dzisis1986
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I did the version of DESeq2 but i would like a simpler way with ggplot lets say. I want to see the PCA before normalization with DESeq2. Wh…
Comment: SNPid or chromosomal number and position in vcf
by
Nai
▴
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Sorry, Here SNP.txt is converted .vcf file for MatrixEQTL. The format is:
id Genotype1 Genotype2 Genotype3 Genotype4 Genotype5 Genotype6 rs…
Comment: Snakemake error in gatk pipeline
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kamanovae
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But if you remove all flags with a value of -8.00, then the same error appears with a different value
/bin/bash: -12.50: No such file …
Comment: PCA from gene count matrix with two conditions
by
ATpoint
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All you need is in https://bioconductor.org/packages/release/bioc/html/PCAtools.html
Or even simpler run the DESeq2 code for PCA and selec…
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