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Extracting upstream and Downstream of a Gene based on different intervals

intervals upstream written 21 days ago by always_learning • 890 • updated 21 days ago by sacha • 1.2k

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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 7 months ago by bioinforesearchquestions • 140 • updated 7 months ago by Sean Davis ♦ 24k

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Change list of consecutive genomic coordinates to intervals?

R intervals sequence written 7 months ago by patrick.turko • 10 • updated 7 months ago by Charles Plessy • 2.5k

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

bedtools footprint intervals slop written 15 months ago by Ian ♦ 5.2k • updated 15 months ago by Alex Reynolds ♦ 24k

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Statistics on BED files

bed intervals statistics written 16 months ago by abedkurdi10 • 20 • updated 16 months ago by Alex Reynolds ♦ 24k

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Recent Replies

A: FlexiDot: highly customizable, ambiguity-aware dotplots by toheitka • 160
# New [FlexiDot](https://github.com/molbio-dresden/flexidot) version released: ## Annotation-base...
C: How to manage self loops in gene coexpression network constructed from RNA-seq d by Kevin Blighe ♦ 21k
Good point, zx8754
A: how to get read density for the first 1000 nt of each transcript by Devon Ryan ♦ 80k
About 22 months too late, but using deepTools: 1. Use `bamCoverage` to get a bigWig of the files...
C: How to manage self loops in gene coexpression network constructed from RNA-seq d by zx8754 ♦ 4.5k
Maybe *diag* is safer? diag(cormat) <- NA --------- Other useful functions: `lower.tri`...
C: haplotypecaller can not run in single bam file by genomax ♦ 49k
What does that mean? Can you provide the actual commandline you used?
A: reasons for htseq-count with zero features by genomax ♦ 49k
Have you looked at the alignment report for that sample and if so what does it say. Perhaps you r...
C: Pathway enrichment with differential expression p-values by DVA • 450
Thanks so much for the information!
C: Issue using MaSuRCA-3.2.6 by Kevin Blighe ♦ 21k
Okay, apologies that I could not assist in this case. I would contact the developers, but chances...
C: How to manage self loops in gene coexpression network constructed from RNA-seq d by Kevin Blighe ♦ 21k
Clustering algorithms will just cluster whatever data you provide. To remove self-loops, you can ...
C: Stringtie output files by Kevin Blighe ♦ 21k
I should additionally point out that *DDX11L1* is a pseudogene. So, it makes sense that it may ha...
C: Applying a function to a matrix by zx8754 ♦ 4.5k
Absolutely **no** reason to use `apply` in this case, simple `2^log.data` is about 200x faster. (...
A: Pathway enrichment with differential expression p-values by b.nota • 3.9k
There is a nice review in [Plos Comp][1] about the different methods that are available for pathw...

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