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Recent Replies
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴
60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file
by
ramiro.barrantes
•
0
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
by
ntsopoul
▴
60
![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
by
ntsopoul
▴
60
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
by
ATpoint
82k
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
by
ntsopoul
▴
60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
by
J.
▴
40
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs?
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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:…
Answer: Biomart issue, why so few 3'utrs?
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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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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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Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
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The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
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The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
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