What it does

This tool takes a SAM file and a TXT file with start and stop positions as input and prints all tags of reads that overlap with regions to user specified output file.

Input

Dataset 1: SAM file of aligned reads.

Dataset 2: Tab delimited TXT file with start and stop positions.

90	633
659	1140
1144	1561

Output

The output is a blank delimited TXT file of tags of all reads that overlap the user-specified regions with start_stop in the first column and the tag in the second column.

87_636	AAATCAAAGTATGAATGAAGTTGCCT
87_636	AAATTCATAGCATTAATTTCAACGGG
656_1143	GGGGCAGCCATATTGGCAATTATCAT

About Author

Author: Gundula Povysil, MD, PhD

Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria

Contact: gpovysil@gmail.com