Python >= 3.6pysamBiogffuitlsrequeststqdm
pip install jla-tailerGlobal 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