2014-06-27
 
    alleleCombination_list = choseAlleleCombination(selectedAllele_list, effective_mapped_reads_dict, primer_start, primer_end)  
   
   
  printOutMappabilityPerExon(effective_mapped_reads_dict, project_folder):
 

2014-06-26

Function: generateExonAlignmentInfo(scratch_folder, output_id, exons_boundary_dict, equipment_id, alignmentLengthCutoff)

TODO

1. add a function named paired_mapping_reads_dict

key: short read ID
value: a list, should have two element, one forward read info and one reverse read info

2014-06-18

Converting SAM directly to a sorted BAM file

Like many Unix tools, SAMTools is able to read directly from a stream i.e. stdout.

samtools

samtools view -bS file.sam | samtools sort - file_sorted

1440  samtools view -bS DPB1_13\:01.report.bowtie2.sam | samtools sort - DPB1_13_01

 1442  samtools index DPB1_13_01.bam DPB1_13_01.bai