| Topic: | MIT BIG meeting: bcbio and CWL (http://openwetware.org/wiki/BioMicroCenter:BIG_meeting) |
| Time: | Nov 2, 2017 11:00 AM (GMT-4:00) Eastern Time (US and Canada) |
| Location: | MIT Koch Biology Building 68-156 (http://whereis.mit.edu/?go=68) or online |
| Online: | https://zoom.us/j/223311944 |
| Telephone: | US: +1 646 876 9923 or +1 669 900 6833 or +1 408 638 0968 or international https://zoom.us/zoomconference?m=qoCDInqg9wlWdANSN9knRp5E41dRbRhy |
| Meeting ID: | 223 311 944 |
| Recording: | https://youtu.be/nJEDS9Qol8M |
| Slides: | https://github.com/chapmanb/bcbb/blob/master/talks/big2017_bcbio_cwl/big2017_bcbio_cwl.pdf |
Jeff S Jasper jasper1918
chapmanb
/ big2017_bcbiocwl_abstract.md
Last active
November 16, 2017 19:47
BIG meeting at MIT: bcbio and common workflow language
willtownes
/ refgene2bed.py
Last active
January 30, 2024 16:31
Splits a refGene.txt file into multiple .bed files for various genome features (exon,intron, etc), suitable for input to bedtools coverage
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| """ | |
| Python Script to read in a reference genome of refseq IDs and output several tab-delimited BED (text) files suitable for use with bedtools coverage for counting ChIP-seq reads that map to various gene features. | |
| All output files have the structure expected by bedtools, namely, | |
| CHROM POSITION1 POSITION2 REFSEQ_ID | |
| Possible output files include: | |
| 1. distal promoter (transcription start [-5KB,-1KB]) KB means kilobase pairs, not kilobyte | |
| 2. proximal promoter (transcription start [-1KB,1KB]) | |
| 3. gene body (anywhere between transcription start and transcription end) | |
| 4. transcript (anywhere in an exon)- outputs each exon as a separate line | |
| 5. first 1/3 transcript- outputs each exon as a separate line |