Moderator: Alex Reynolds

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Alex Reynolds20k
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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, 7 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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Answer: A: Average intron length in Drosophila melagnoster
... 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 Reynolds20k
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Comment: C: Find "mean" cluster positions after random sampling of genomic events
... 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 Reynolds20k
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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 Reynolds20k
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Answer: A: Bedtools merge only part of feature that overlaps, not whole feature
... 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 Reynolds20k
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Comment: C: manipulating BED occupancy files' intervals
... 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 Reynolds20k
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Answer: A: How to merge bedGraph records which are next to each other and have the same sco
... 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 Reynolds20k
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Answer: A: blast+ and GnuTLS errors on Mac
... 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 Reynolds20k
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Answer: A: extract the number of reads around TSS
... 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 Reynolds20k
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Comment: C: How to extract all the simple repeats from the hg19 reference genome
... 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 Reynolds20k
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Answer: A: How to extract all the simple repeats from the hg19 reference genome
... 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 Reynolds20k

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