Moderator: Alex Reynolds

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Alex Reynolds18k
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Seattle, WA USA
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http://dropbit.com/
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AlexReynolds
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7 years, 5 months ago
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One of the developers behind the fast BEDOPS suite, whose pug Zac is the bestest pug in the world.

Posts by Alex Reynolds

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Comment: C: closest-Features or closestBed Output to find genes downstream of coordinates
... Those are links to documentation, by the way. So if there is something unclear about what you're getting, please do include your inputs and your runtime options. Otherwise, it's rather difficult to help you. ...
written 5 hours ago by Alex Reynolds18k
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Answer: A: closest-Features or closestBed Output to find genes downstream of coordinates
... [BEDOPS `bedmap`][1] will help you map intervals to annotations. [BEDOPS `closest-features`][2] will help you find the closest element(s) to your intervals of interest. You could use either to solve your problem by piping to `awk`, probably, but I don't really understand your question. Define a clea ...
written 5 hours ago by Alex Reynolds18k
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Comment: C: Compare pairs of key/value of perl hash tables
... Not so much an issue here, probably, but watch out for duplicate keys when you make a custom key like this. ...
written 12 hours ago by Alex Reynolds18k
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Answer: A: How to compare peaks (called by MACS2) within a specific genomic area for two sa
... Given a set of intervals and a set of peaks with some score value, you could use [BEDOPS `bedmap --max-element` or `bedmap --max`][1] to get the maximum scoring peak over the interval, or just the maximum score, respectively: $ bedmap --echo --max-element --delim '\t' intervals.bed peaks.bed &g ...
written 13 hours ago by Alex Reynolds18k
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Answer: A: Compare pairs of key/value of perl hash tables
... I wrote a script that suggests one approach: https://gist.github.com/alexpreynolds/9fc6f75c9516f30233f930077b3639f4 Usage: $ intersect.pl --fileA="A.txt" --fileB="B.txt" > answer.txt This uses Perl's experimental "smartmatch" feature, which can give an annoying warning message that can be ...
written 14 hours ago by Alex Reynolds18k
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Comment: C: What is the most popular programming language used in bioinformatics?
... Recently discussed here: https://www.biostars.org/p/251002/ ...
written 14 hours ago by Alex Reynolds18k
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Comment: C: Identifying gene parts based on genomic regions
... Run `cat -te test.bed | head` to make sure your file doesn't have extra tabs or non-Unix line endings. Then fix the file if it does. Then sort the fixed file. ...
written 18 hours ago by Alex Reynolds18k
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Answer: C: Transcript Id conversion
... Ensembl BioMart instructions might help you: http://www.ensembl.org/Help/Faq?id=125 ...
written 1 day ago by Alex Reynolds18k
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Comment: C: Solutions for genomic dataset storage?
... Compression and encoding. Algorithms will always beat hardware. ...
written 2 days ago by Alex Reynolds18k
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Answer: A: Identifying gene parts based on genomic regions
... With [BEDOPS][1], you can convert an annotation file to BED with `convert2bed` and then do a `bedmap --echo-map` operation on it to find overlaps. For example, here's how to get a set of Gencode v21 annotations into BED format: $ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/relea ...
written 2 days ago by Alex Reynolds18k

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