Tool to find 3' tailing of non-coding RNAs
Project description
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.
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