adomingues / filterReads

Filter alignments on sequence length and/or identity of first nucleotide.

Set of tools to select alignments based on:

• length
• first nucleotide of sequence read

This is particularly useful for the analysis of C. elegans small RNA analysis which have fairly specific properties.

The main script is filterReads/filterSmallRNAclasses.py. Another script, filterReads/summarizeNucleotideByReadLenght.py will determine the frequency of each nucleotide per read length from any bam file.

Use case and tutorial to come.

Dependencies

• pysam (working with 0.8.1)