Shicheng Guo Shicheng-Guo

## mds.jpg

      
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## refgene2bed.py
"""
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
	"""
	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