Shicheng Guo Shicheng-Guo
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 |
