Moderator: Alex Reynolds

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Alex Reynolds21k
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Seattle, WA USA
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http://dropbit.com/
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AlexReynolds
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49 minutes ago
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7 years, 11 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: how to find genes based on SNP rsIDs
... If you want a fast (binary) search with a locally-stored dataset, where you know exactly what SNPs and gene annotations are being queried, here's a way to set up files to do your own querying, which scales up very well when you have a lot of SNPs. 1) Get annotations of interest and write them into ...
written 57 minutes ago by Alex Reynolds21k
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Comment: C: how to make a .tbi file of .gtf.gz?
... Another option: $ gunzip -c foo.gtf.gz | gtf2bed - | bgzip -c > foo.bed.gz $ tabix -p bed foo.bed.gz ...
written 4 hours ago by Alex Reynolds21k
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Comment: C: awk one line command
... Note that `grep chr1 input.bed` will return records for `chr1`, `chr10`, `chr11`, etc. and `grep chr2 input.bed` will return records for `chr2`, `chr20`, and `chr21`, so the output for those search keys will contain more intervals than probably expected and is likely incorrect. ...
written 1 day ago by Alex Reynolds21k
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Comment: C: bedtools window - killed: 9 error
... If you do the second approach that uses standard Unix streams, then BEDOPS only uses ~2 GB of RAM, not 30 GB as other approaches may require. You can adjust this memory usage downwards, which is due to sorting, via `--max-mem=` in `convert2bed` or `vcf2bed`, if you have less than 4GB of RAM. Final d ...
written 1 day ago by Alex Reynolds21k
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Answer: A: bedtools window - killed: 9 error
... Another option: $ gunzip -c chr1.vcf.gz | vcf2bed --sort-tmpdir="/some/large/dir" > chr1.bed $ bedmap --echo --count --delim '\t' 50kb.bed chr1.bed > answer.bed $ rm chr1.bed Or to avoid creating an intermediate file: $ bedmap --echo --count --delim '\t' 50kb.bed <( gunzi ...
written 1 day ago by Alex Reynolds21k
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Answer: A: VCF to BED conversion error in BEDOPS
... If `/tmp` is filling up, use `--sort-tmpdir=` with `convert2bed` to specify an alternate directory to store intermediate sort data. You could use `--do-not-sort`, I suppose, but really you want a sorted BED file so that you can use it for set operations. If you use `--do-not-sort`, you would follo ...
written 1 day ago by Alex Reynolds21k
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Answer: A: awk one line command
... You need to prefix the `chr` variable with the string literal `chr`, as right now you are asking `awk` to match the first field on numbers (1 through 22) and not chromosome names (chr1 through chr22). $ for chr in {1..22}; do awk -v chr="chr${chr}" ... But BEDOPS offers a much faster and simpl ...
written 1 day ago by Alex Reynolds21k
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Comment: C: vcf files: counting number of variants in genomic windows of chosen size
... The file `chr21.vcf.gz` is not a VCF file, but is instead a gzip-compressed binary. Extract it and then pipe the extracted data to `vcf2bed`, e.g.: $ bedmap --echo --count --delim '\t' windows.bed <(gunzip -c chr21.vcf.gz | vcf2bed -) > windows_with_counts_of_variants.bed Interpretation: ...
written 2 days ago by Alex Reynolds21k
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Answer: A: vcf files: counting number of variants in genomic windows of chosen size
... Via BEDOPS: $ bedmap --echo --count genes.bed <(vcf2bed < variants.vcf) > answer.bed If your genes are in another format, say GFF: $ bedmap --echo --count <(gff2bed < genes.gff) <(vcf2bed < variants.vcf) > answer.bed If you have generic windows, replace `genes.be ...
written 3 days ago by Alex Reynolds21k
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Comment: C: common transcription factor for a list of gene in Arabidopsis thaliana.
... I wish I could help more, but I haven't worked with Arabidopsis data much, really. My answer's more of a generic approach. Maybe there are Arabidopsis-specific mailing lists or forums where people know about curated or pre-calculated datasets (https://www.arabidopsis.org/help/faq.jsp) — or perhaps a ...
written 13 days ago by Alex Reynolds21k

Latest awards to Alex Reynolds

Scholar 1 day ago, created an answer that has been accepted. For A: How to create a new bigwig file defined by a subset of bed file?
Appreciated 1 day ago, created a post with more than 5 votes. For A: How To Sort Bed Format File
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: How To Sort Bed Format File
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: How Do You Store And Share Your Bioinformatics Data? (Fasta, Fastq, Sff, Etc.)
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Memory Efficient Bedtools Sort And Merge With Millions Of Entries?
Scholar 4 weeks ago, created an answer that has been accepted. For A: vcf2bed argument in bedops partially process vcf file
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Converting a VCF with SNPs and indels to BED format
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: vcf2bed argument in bedops partially process vcf file
Scholar 4 weeks ago, created an answer that has been accepted. For A: vcf2bed argument in bedops partially process vcf file
Scholar 4 weeks ago, created an answer that has been accepted. For A: vcf2bed argument in bedops partially process vcf file
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Sort Bed Format File
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: vcf2bed argument in bedops partially process vcf file
Scholar 4 weeks ago, created an answer that has been accepted. For A: vcf2bed argument in bedops partially process vcf file
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Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: How To Create Mutation Diagram In R Or In Any Tools?
Scholar 7 weeks ago, created an answer that has been accepted. For A: extracting a specific field from .bed file and sort into new file
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Scholar 8 weeks ago, created an answer that has been accepted. For A: Checking the quality and reliability in bioinformatics

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