jla-tailer 0.1.5

Tool to find 3' tailing of non-coding RNAs

Tailer: A tool for 3' end analysis of non-polyadenylated RNAs from 3' sequencing data

Requirements

• Python >= 3.6
• pysam
• Bio
• gffuitls
• requests
• tqdm

Installation

pip install jla-tailer

Usage

Global alignment with a GTF annotation and SAM/BAM formatted files

Tailer -a [GTF Annotation] [SAM or BAM Files]

Local alignment with with FASTA/Q and specific Ensembl IDs of interest or reference fasta

Tailer -e [comma separated list of EnsIDs no spaces] [FASTA/Q files]
Tailer -f fasta_reference_file.fasta [FASTA/Q files]

Optional arguments

• -t, --threshold [int, default=100]
  • Any alignment identified further than this distance in nucleotides from the mature end will be considered spurious and discarded
• -x, --trim [int, default=0]
  • Helper for local mode only, can remove X nucleotides from adapter on the 3' end
• -r, --rev_comp
  • Helper for local mode only. If set, will reverse complement the reads which is necessary for the Lykke-Andersen pipeline
• -f, --fasta
  • Use a fasta file as a reference instead of building one from ensembl IDs (Local Only)
• -s, --sequence
  • Output sequence in the tail file. Useful for debugging.