jla-tailer 0.1.18

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]

Required Arguments

• -a, --annotation
  • GTF formatted database to be used to infer 3' ends. Ensembl GTFs have worked well for this pipeline
• [SAM or BAM Files]
  • Space separated list of sam/bam formatted file locations to perform 3' end tail analysis

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]

Required Arguments

• -e, --ensids
  • Comma separated list of ensembl IDs. Either -e or -f inputs are required.
• -f, --fasta
  • FASTA formatted file to align reads against. Either -f or -e inputs are required
• [Trimmed FASTQ files]
  • Space separated FASTQ file locations for analysis.

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
• -read, --read [int, default=1]
  • Paired end only. 1 or 2 to signify which end contains the 3' end information.
• -r, --rev_comp
  • If set, will reverse complement the reads. Necessary for some library prep methods
• -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.

miRNA tailing (in development)

Tailer --miRNA [sam files]

Determines tails using an alignment file (SAM/BAM) that was aligned to a fasta genome of mature miRNAs

Optional arguments

• --rpad [int, default=0]
  • Number of downstream nucleotides added to distinguish between post-transcriptional and genome-encoded tails