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Recent Replies
Comment: Where to get the following bed file?
by
wyuan37
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0
Hi, I emailed them and did get the bed file! Thank you so much.
Answer: Post-imputation QC for input into GWAS analyses
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LauferVA
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1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
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GenoMax
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You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object
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ntsopoul
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does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
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ramiro.barrantes
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Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object
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ntsopoul
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![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content
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ntsopoul
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I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: Overlapping Ranges within Granges object
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ATpoint
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I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object
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ntsopoul
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I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
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J.
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FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
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GenoMax
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AFAIK "MANE" project is only for human protein-coding genes.
One potential explanation. Out of the 2000 ID's only 125 may be MANE.
https:…
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i.sudbery
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The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
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ATpoint
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Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
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