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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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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
<img src="https://i.ibb.co/M8TCL9c/Upvote-Bookmark-Accept.png" alt="upvote_bookmark_accept" border="0" width="400px">
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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