Moderator: Alex Reynolds
Alex Reynolds ♦ 20k
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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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... Untested, but I think it should work, in theory:
Retested with the updated link from genomax:
$ wget -qO- ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/dmel-all-intron-r6.16.fasta.gz | gunzip -c - | awk '{ />/ && ++a || b += length(); } END { print b/a; }'
...
written 8 hours ago by
Alex Reynolds ♦ 20k
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... You could pipe the output of a `bedmap --echo-map` to a `bedmap --merge` operation to get a common genomic range for overlapping intervals within a pairwise combination.
I don't know what a "mean" genomic range is, however. Maybe you could investigate piping `bedmap --echo-map-size` to `calc` or s ...
written 9 hours ago by
Alex Reynolds ♦ 20k
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Answer:
A: Finding Kmers From Fasta File
... I wrote a command-line k-mer counter called `kmer-counter` that will output results in a form that a Python script can consume: https://github.com/alexpreynolds/kmer-counter
You can grab, build and install it like so:
$ git clone https://github.com/alexpreynolds/kmer-counter.git
$ cd kmer- ...
written 10 hours ago by
Alex Reynolds ♦ 20k
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... See BEDOPS `bedops --partition`: http://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html#partition-p-partition
You'll need to munge your input into a correctly-ordered and `sort-bed`-sorted BED file, run the partitioning, and then follow up with `bedmap` to apply annotat ...
written 11 hours ago by
Alex Reynolds ♦ 20k
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... You appear to use the `--mean` option on input that will not have score data in the fifth column. It looks like there is no numerical score or signal information in the fifth column of `sorted.bed`. I would check that input or remove `--mean`. ...
written 1 day ago by
Alex Reynolds ♦ 20k
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... Via [BEDOPS][1], `bash` and GNU core utilities:
$ SORTED_BEDGRAPH=in.bedGraph
$ while read -r score; do awk -v s=$score '$4==s' ${SORTED_BEDGRAPH} | bedops --merge - | awk -v s=$score '{print $0"\t"s}'; done < <(cut -f4 ${SORTED_BEDGRAPH} | sort | uniq) | sort-bed - > answer.bed
T ...
written 1 day ago by
Alex Reynolds ♦ 20k
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... On a Mac. install [Homebrew][1], then run `brew install libgnutls`. On CentOS 7, you could run `sudo yum install gnutls-devel`. If this is a dependency issue, either of these will install the [GnuTLS][2] library.
[1]: https://brew.sh/
[2]: http://www.gnutls.org/ ...
written 1 day ago by
Alex Reynolds ♦ 20k
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... Via [BEDOPS][1]:
$ bedmap --echo --count TSSs.bed <(sam2bed < reads.sam) > answer.bed
If you want to pad the TSSs, say by 1k bases on both sides, add the `--range N` option:
$ bedmap --echo --count --range 1000 TSSs.bed <(sam2bed < reads.sam) > answer.bed
This will like ...
written 6 days ago by
Alex Reynolds ♦ 20k
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... It's unclear to me what parameters were used to generate these files. The [best people to ask][1] would probably be the Repeatmasker folks.
[1]: http://www.repeatmasker.org/cgi-bin/form2mail?template=feedback.tmpl&title=Feedback%20Form ...
written 6 days ago by
Alex Reynolds ♦ 20k
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... You could download repeats for hg19 from the [Repeatmasker][1] folks and convert to BED with `convert2bed` to do set operations:
$ wget -qO- http://www.repeatmasker.org/genomes/hg19/RepeatMasker-rm405-db20140131/hg19.fa.out.gz | gunzip -c - | convert2bed --input=rmsk - > hg19.fa.out.bed
You ...
written 6 days ago by
Alex Reynolds ♦ 20k
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