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Recent Votes

A: Ballgown Error in file(file, "rt") : invalid 'description' argument

Answer: ATAC seq analysis

A: What is a suitable LD threshold for LD pruning of snp data?

Answer: Problems installing cutadapt with conda

A: Pruning a VCF file and extracting pruned in snps using bcftools

Comment: Editing FASTQ headers

Comment: plink bim file stops at chrM

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Scholar to rpolicastro 8.1k

Popular Question to rob234king ▴ 600

Recent Replies

Comment: Problems installing cutadapt with conda by Camila Martínez ▴ 30

Thanks. I didn't know about the "Accept" button. I just did it.

Comment: plink bim file stops at chrM by rturba ▴ 10

Hmmmmmmmmmmmm... It's because the way this genome was defined was that chr19 is the chrX. So I renamed from chrXIX to X and therefore it sk…

Comment: plink bim file stops at chrM by chrchang523 9.2k

That's due to your incorrect use of `--chr-set 20`.

Comment: Editing FASTQ headers by iraun ★ 4.3k

Yes of course the code can be shortened :).

Comment: Beginners bioinformatics project with machine learning? by godwin ▴ 50

Thank you so much. You were really helpful.

Comment: plink bim file stops at chrM by rturba ▴ 10

Actually, (sorry @chrchang523, this seems like a never ending issue!), I've just checked my BIM output and there seems to be an issue with …

Comment: Retrieving ensembl protein length with biomart by iatz ▴ 10

That's perfect, I can as well use directly CDS length for my purposes, thanks !

Answer: Select a list of reads in IGV by Pierre Lindenbaum 144k

you can add a YC tag in the reads you want: https://software.broadinstitute.org/software/igv/ReleaseNotes/2.4.x > 3. Alignment colori…

Comment: Which statistical test should be used for comparison of a single gene expression by Ram 36k

You're talking about comparing two numbers in a statistically significant way. I don't think that's possible.

Comment: ATAC seq analysis by Ram 36k

Comment: ATAC seq analysis by aranyak111 • 0

Thanks, the suggestion has solved the problem for now.

Comment: How to use vcfuniq from vcflib? by kshaffman • 0

Hi Pierre, Could you please give me more information on how I could use bcftools isec to accomplish my goal?

Comment: Parsing SAM files with java by Pierre Lindenbaum 144k

duplicate: https://www.biostars.org/p/207657/

Answer: ATAC seq analysis by Ram 36k

You have not assigned a value to `indexForSubread`. Add this lines based on your previous code to the script: indexForSubread <- "ATAC…

Comment: plink bim file stops at chrM by rturba ▴ 10

Awesome! Thank you so much for the help. When I defined `--chr-set 20 #20 autosomal (excluding chrUn)`, and the `--allow-extra-chr`, I was …

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