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README.md

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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)