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Gordon Smyth
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Recent Replies
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
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20
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…
Comment: I need help with a methyl array data analysis
by
prasundutta87
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650
Did you come across this?
https://www.biostars.org/p/432297/
Regards,
Prasun
Comment: Single cell chemistry
by
David
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0
Unlikely, this data came from a experienced sequencing team, I 'm the inexperienced data analyst.
I'm not sure if these samples are 10x, …
Comment: Single cell chemistry
by
David
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0
Sorry, I did not explain it well.
I did it before with other group of samples and different chemistry, so cellranger is working fine in my…
Comment: Do bioinformaticians often break molecular biologists' hearts by being the first
by
jli.ww
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0
Based on my personal experience as a computational biologist, I was not a co-first author even if I prioritized the candidates from the pub…
Answer: ScRNA data
by
Dr William Klubinski
▴
20
It seems like your single cell RNAseq data does not already contain the Cell Barcodes or Unique Molecular Identifiers in the standard way -…
Comment: Demultiplexing bam file
by
GenoMax
129k
> Part of the header of the bam file
So perhaps there are more samples.
https://www.biostars.org/u/21477/: `grep "SM*" header_of_bam`. Is…
Answer: extract all fasta sequence from db v5
by
GenoMax
129k
If you need the fasta sequence download from NCBI here (146 GB zip compressed file) : https://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
Comment: ScRNA data
by
GenoMax
129k
Is this from a SRA dataset? If so it is possible that you can get the correct information in `DataAccess` tab. Provide the accession number…
Comment: extract all fasta sequence from db v5
by
Pierre Lindenbaum
154k
is version 4 compatible with blast v5 ? try to use version 4....
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