What it does

This tool will fetch flanking regions around STRs from the reads output by "STR detection" step, screen for quality score at STRs and adjacent flanking regions, and output two fastq files containing flanking regions in forward-forward direction.

• This tool assumes that the quality score is Phred+33, such as Sanger fastq.
• Reads that have either left or right flanking regions shorter than the length of flanking regions that require quality screening will be removed.

Citation When you use this tool, please cite Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research

Input

The input file needs to be in the same format as output from STR detection step. This format contains length of repeat, length of left flanking region, length of right flanking region, repeat motif, hamming (editing) distance, read name, read sequence, read quality score

Output

The output will be two fastq files. The first file contains left flanking bases. The second file contains right flanking bases.

Example

• Starting with this test input

  6       40      54      G       0       SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1     TACCCTCCTGTCTTCCCAGACTGATTTCTGTTCCTGCCCTggggggTTCTTGACTCCTCTGAATGGGTACGGGAGTGTGGACCTCAGGGAGGCCCCCTTG    GGGGGGGGGGGGGGGGGFGGGGGGGGGFEGGGGGGGGGGG?FFDFGGGGGG?FFFGGGGGDEGGEFFBEFCEEBD@BACB*?=99(/=5'6=4:CCC*AA
  

• If we want to get fastq files of flanking regions around the detected STRs with quality score of at least 20, the program will report these two fastq files

  @SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
  TACCCTCCTGTCTTCCCAGACTGATTTCTGTTCCTGCCCT
  +SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
  GGGGGGGGGGGGGGGGGFGGGGGGGGGFEGGGGGGGGGGG
  
  
  @SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
  TTCTTGACTCCTCTGAATGGGTACGGGAGTGTGGACCTCAGGGAGGCCCCCTTG
  +SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
  GGGGG?FFFGGGGGDEGGEFFBEFCEEBD@BACB*?=99(/=5'6=4:CCC*AA