# README on operation_N_filter.txt and merging bam files
# Tonatiuh Pena Centeno and Katharina J. Hoff
# June 26th 2012

The file operation_N_filter.txt is a bamtools filter that will discard all entries from a bam file that contain the letter N in the CIGAR string. (In terms of gene structures, Ns reflect long introns.)

Usage example:
bamtools filter -in toyAlignments.bam -out toy.withoutN.bam -script operation_N_filter.txt

Furthermore, we shortly document how to join bam files:
bamtools merge -in eg1.bam -in eg2.bam -out eg.merged.bam
