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PeterKW
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Recent Replies
Comment: problems with MAF for MutSigCV (vcf2maf)
by
RAJDEEP
•
0
The above code has helped me a lot and it works, in a typical vcf file in the last column of the header TUMOUR and NORMAL are written. befo…
Comment: Single cell chemistry
by
swbarnes2
13k
OP could cheat a bit by adding an A to the end of every read of R1 (and a suitable letter to the quality string) and see if Cellranger can …
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Camilo Andres
▴
30
So sorry, is data from the TCGA project. The only columns of data it has, are Hugo symbols, Gene Entrez IDs and Tumor Sample Barcodes. I do…
Comment: Error in download library file in expression console software
by
GenoMax
129k
What software is this referring to?
Comment: Single cell chemistry
by
GenoMax
129k
As you can see the data is one base short. If cell ranger is unable to analyze the data you may need to look elsewhere.
Comment: Bioinformatics Master's Student
by
Mensur Dlakic
★
23k
`Bioinformatics Master's Student` is not an informative title for your question. I imagine most people will ignore it by assuming that this…
Comment: Why coordinate sort is required in sambamba depths?
by
Pierre Lindenbaum
154k
> what coordinate sorting is exactly?
https://www.biostars.org/p/319730/#319750
> Why coordinate-sort is required
coordinate sort is de …
Comment: Bioinformatics Master's Student
by
Nada
•
0
why the read is like this ??
I know I should contains (ATGC) not (T2200330123010111..03100022.....023..02.....011022.)
Comment: Single cell chemistry
by
swbarnes2
13k
As far as I know, v2 must mean 10x. But if it the cell barcode + umi is 26 bases, you don't have that.
Comment: best annotation approach for peaks
by
Chironex
▴
40
Hi, I don't understand why, if I change TSS +1000/-1000 or +3000/-3000 or +10.000/-10.000 the number of regions annotated is the same. More…
Comment: I need help with a methyl array data analysis
by
Ahmad
▴
10
I actually have replicates.
thank you
Comment: Why are some WES VCFs larger than others?
by
Jeremy Leipzig
21k
"It's not a gvcf with site coverage for the entire cohort, I called the variants myself"
This sentence doesn't make sense to me. gVCFs are …
Comment: I need help with a methyl array data analysis
by
Dr William Klubinski
▴
30
It seems the data appears to be in the beta value format (?), which represents the proportion of methylated probe intensity over the total …
Comment: problem of Global Biobank Meta-analysis Initiative
by
Fabio Marroni
★
3.0k
Hi, can you please add the link to the page you mentioned? AFAIK some data have restricted access. Maybe full GWAS data belongs to this cat…
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