Open shengdar opened 7 years ago
I would love to have this read length option, as 75bp paired-end by NextSeq is much more cost effective than MiSeq.
For now, I suspect I may change the parameters on reading cigar in "findCleavageSites.py" file?
I really appreciate if you could support this by manifest option.
"Current findCleavageSites.py"
for cigar_operation in read.cigar: # Identify positions that end in position 151 and start at position 151 # Note strand polarity is reversed for position 151 if cigar_operation.type == 'M': if ((cigar_operation.query_from <= 146 - start_threshold) and (151 - start_threshold <= cigar_operation.query_to)): first_read_cigar = cigar_operation first_read_chr = cigar_operation.ref_iv.chrom first_end = min(cigar_operation.query_to, 151) distance = first_end - cigar_operation.query_from first_read_position = cigar_operation.ref_iv.start + distance - 1 first_read_strand = '-' if ((cigar_operation.query_from <= 151 + start_threshold) and (156 + start_threshold <= cigar_operation.query_to)): second_read_cigar = cigar_operation second_read_chr = cigar_operation.ref_iv.chrom second_end = max(151, cigar_operation.query_from) distance = second_end - cigar_operation.query_from second_read_position = cigar_operation.ref_iv.start + distance second_read_strand = '+'
"Something like this for 75bp paired reads?"
for cigar_operation in read.cigar: # Identify positions that end in position 76 and start at position 76 # Note strand polarity is reversed for position 76 if cigar_operation.type == 'M': if ((cigar_operation.query_from <= 71 - start_threshold) and (76 - start_threshold <= cigar_operation.query_to)): first_read_cigar = cigar_operation first_read_chr = cigar_operation.ref_iv.chrom first_end = min(cigar_operation.query_to, 76) distance = first_end - cigar_operation.query_from first_read_position = cigar_operation.ref_iv.start + distance - 1 first_read_strand = '-' if ((cigar_operation.query_from <= 76 + start_threshold) and (81 + start_threshold <= cigar_operation.query_to)): second_read_cigar = cigar_operation second_read_chr = cigar_operation.ref_iv.chrom second_end = max(76, cigar_operation.query_from) distance = second_end - cigar_operation.query_from second_read_position = cigar_operation.ref_iv.start + distance second_read_strand = '+'
Update manifest to support different read lengths (for example paired end 75 instead of 150)