Moderator: Alex Reynolds

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Alex Reynolds24k
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Seattle, WA USA
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http://dropbit.com/
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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: dna compression cod
... If you're strictly talking about generic DNA, you might look into the 2bit and nib formats: http://genome.ucsc.edu/FAQ/FAQformat.html#format7 Ignoring ambiguous bases, you can encode the four bases of DNA (A, C, G, T) with two binary bits like so: A : 00 C : 01 G : 10 T : 11 Consi ...
written 15 hours ago by Alex Reynolds24k
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Answer: A: perl compilation errors
... Break up that Perl one-liner into something you can debug line by line. ...
written 8 days ago by Alex Reynolds24k
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Comment: C: how can I transfer this different steps bedgraph format into 1bp file?
... To get an ad-hoc subset, you can use set operations in a Unix pipeline: $ echo -e 'chr2\t1\t7' | bedops -e 1 foo.bed - | bedops --chop 1 - | bedmap --faster --echo --echo-map-id --delim "\t" - foo.bed | cut -f1,2,4 > answer.txt The `--faster` option can be used here, as none of your example ...
written 9 days ago by Alex Reynolds24k
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Answer: A: GREP: out of memory
... To have `grep` do exact-word matches from a file of strings, use `-w -F`: $ grep -w -F -f 1.txt 2.gff > 3.gff The `-w` option does word searches using regular expressions. The `-F` option modifies this to do exact-string matching. Using `-w` on its own will consume a lot of memory, becaus ...
written 9 days ago by Alex Reynolds24k
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Answer: A: Identify reads that span intron-exon junctions in RNA-Seq
... Steps via `awk` and [BEDOPS][1]. Build a BED file of exons: $ wget -qO- ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gtf.gz \ | gunzip -c - \ | awk '($3=="exon")' - \ | gtf2bed - \ | cut -f1-6 - \ > gencode ...
written 9 days ago by Alex Reynolds24k
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Answer: A: how can I transfer this different steps bedgraph format into 1bp file?
... If you want to use set operations: $ bedops --chop 1 foo.bed | bedmap --faster --echo --echo-map-id --delim "\t" - foo.bed | cut -f1,2,4 > answer.txt ...
written 9 days ago by Alex Reynolds24k
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Comment: C: TukeyHSD does not match the box plot
... Perhaps make notched box plots to more directly do comparisons of medians between two groups. https://www.jstor.org/stable/2683468?seq=1#page_scan_tab_contents ...
written 10 days ago by Alex Reynolds24k
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Answer: A: Find overlap between bam and gff
... Convert to BED via `convert2bed` helper scripts: $ gff2bed < annotations.gff > annotations.bed $ gff2bed < rmsk.gff > rmsk.bed $ bam2bed < reads.bam > reads.bed If you want at least X reads that overlap annotations that do not overlap repeatmasked regions: $ X=12 ...
written 10 days ago by Alex Reynolds24k
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Answer: A: Merge multiple BED files (multiple intersect) with average score
... To do this efficiently, you can use `bedops` and `bedmap` to calculate this over N files (N=57, in your case). $ bedops -u A.bed B.bed ... N.bed > union.bed $ bedops -m A.bed B.bed ... N.bed > merge.bed $ bedmap --echo --mean --delim "\t" merge.bed union.bed > answer.bed The f ...
written 11 days ago by Alex Reynolds24k
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Answer: A: Find out over-represented nucleotides
... Look at the `seqLogo` package in Bioconductor. https://bioconductor.org/packages/release/bioc/html/seqLogo.html You could use the `ic` property of a `seqLogo` object: https://bioconductor.org/packages/release/bioc/vignettes/seqLogo/inst/doc/seqLogo.pdf If you are comfortable with the command line, ...
written 13 days ago by Alex Reynolds24k

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Teacher 2 days ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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Scholar 15 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
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Scholar 8 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
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Scholar 9 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
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Scholar 9 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper

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