McIntyre Lab Scripts

This is a collection of python scripts that we use for handling various types of genomic data. Additional information can be found at McIntyre Scripts Documentation.

Name		Name	Last commit message	Last commit date
Latest commit History 400 Commits
doc		doc
mclib_Python		mclib_Python
.gitignore		.gitignore
.gitmodules		.gitmodules
LICENSE		LICENSE
README.md		README.md
SeparateLast.py		SeparateLast.py
SizeChecker.py		SizeChecker.py
bed2fasta.py		bed2fasta.py
blastParseAmbiguityFlags.py		blastParseAmbiguityFlags.py
blatParser.py		blatParser.py
buildFusions.py		buildFusions.py
calcGCContent.py		calcGCContent.py
catTable.py		catTable.py
combineMileup.py		combineMileup.py
combineMpileupNoQual.py		combineMpileupNoQual.py
count_total_uniq_fq.py		count_total_uniq_fq.py
extractJunctions.py		extractJunctions.py
fasta2bed.py		fasta2bed.py
fastaSample.py		fastaSample.py
fastq2fasta.py		fastq2fasta.py
fastqDumpCoords.py		fastqDumpCoords.py
fastqSplitDups.py		fastqSplitDups.py
identify_distinct_fusions.py		identify_distinct_fusions.py
identify_duplicates.py		identify_duplicates.py
identify_duplicates_hashed_noDic.py		identify_duplicates_hashed_noDic.py
identify_homopolymers.py		identify_homopolymers.py
identify_quality.py		identify_quality.py
logParser.py		logParser.py
mpileup2wig.py		mpileup2wig.py
parseBlastXml.py		parseBlastXml.py
parse_BWA_sam_file.py		parse_BWA_sam_file.py
parse_gff_to_transcript_bed.py		parse_gff_to_transcript_bed.py
parse_gff_to_tss_bed.py		parse_gff_to_tss_bed.py
plotTiles.py		plotTiles.py
rpkm_calculate.py		rpkm_calculate.py
sam_compare.py		sam_compare.py
simulate_reads.py		simulate_reads.py
simulate_snps.py		simulate_snps.py
splitTable.py		splitTable.py
subset_fastq_file_by_ID_list_v3.py		subset_fastq_file_by_ID_list_v3.py
update_mclib.sh		update_mclib.sh
vcfCountSnps.py		vcfCountSnps.py
vcfFastaUpdate.py		vcfFastaUpdate.py
wigglePlot.py		wigglePlot.py

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McIntyre-Lab/mcscript

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