README

ExtractFlankingSequence : Grab reference genome sequence 5' flanking or at 5' end of short reads mapped to a reference genome

Extract1stNBasesFromMappedReads.py: Grab 1st N bp from reads mapped to reference genome

CompareExtractedFiles.py: Compare results from the two scripts listed above

DEPENDENCIES

Python 2.7 pyfasta numpy

USAGE

python ExtractFlankingSequence.py sam_file reference_sequence.fasta #_bp_to_extract output_file_name python Extract1stNBasesFromMappedReads.py <# bp to extract> python CompareExtracts.py <extract1.fa> <extract2.fa>

e.g.

python ExtractFlankingSequence.py hits.sam dmel-4-chromosome-r5.33.fasta -20 flanks.fasta python ExtractFlankingSequence.py hits.sam dmel.genome.fasta 20 out.fasta GATGGCAT python ExtractFlankingSequence.py flanks.fasta out.fasta compare.fa

David L. Stern Janelia Farm Research Campus 5 February 2013

• Copyright 2013 Howard Hughes Medical Institute.
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• Use is subject to Janelia Farm Research Campus Software Copyright 1.1
• license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html ).