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Extracting upstream and Downstream of a Gene based on different intervals

intervals upstream written 4 months ago by always_learning • 930 • updated 4 months ago by sacha • 1.5k

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Can I merge the exome interval lists from two different kits for identifying CNVs using XHMM?

exome bed intervals xhmm cnvs written 10 months ago by bioinforesearchquestions • 160 • updated 10 months ago by Sean Davis ♦ 25k

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Change list of consecutive genomic coordinates to intervals?

R intervals sequence written 11 months ago by patrick.turko • 10 • updated 11 months ago by Charles Plessy • 2.5k

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535

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How to extend variable length intervals to the same final length?

bedtools footprint intervals slop written 18 months ago by Ian ♦ 5.2k • updated 18 months ago by Alex Reynolds ♦ 25k

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Statistics on BED files

bed intervals statistics written 20 months ago by abedkurdi10 • 20 • updated 20 months ago by Alex Reynolds ♦ 25k

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Recent Replies

A: Performing GSEA using MSigDB gene sets in R by igor ♦ 6.6k
You can try the fgsea package, which is probably most similar to the original GSEA. It can be run...
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Long story short, my suggestion to speed up Star-cufflinks pipeline is to get rid of cufflinks an...
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Sounds weird... than maybe try reinstalling rsem. Or just use `salmon` or `kallisto` on your fast...
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oh thanks a lot, I have scrolled a bit the file but did not go down enough to see the ENSEMBL gen...
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I don't think those are HGNC ID's. They are things which did not have a gene name. > If no ge...
C: gene_Id in ENCODE gene expression table by RamRS ♦ 17k
See: https://www.biostars.org/p/309884/
C: gene_Id in ENCODE gene expression table by fusion.slope • 150
thanks a lot, i think alex already answered my question :) but to confirm i should check rsem out...
C: gene_Id in ENCODE gene expression table by genomax ♦ 56k
This is what [the explanation legend says][1]: Estimated expression levels from RSEM as a tsv fi...
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While I would typically expect the exonic rate to be lower for a ribosome-depleted library versus...
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I assume that you mean copy number alterations in different stages of cancer **in the same patien...
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That's OK - there are frequently similarly worded questions coming from different users. However...
C: gene_Id in ENCODE gene expression table by fusion.slope • 150
For example the tsv file here: https://www.encodeproject.org/experiments/ENCSR000CPH/ click in ...

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