Tailer-processing commands and examples of tail inference. (A) Example commands to run Tailer-processing. After installation with PIP, Tailer-processing can be invoked by typing “Tailer” into the command line. An “-h” flag will provide usage information that is also available in a readme.txt file. Examples of running Tailer-processing in global mode, in local mode using Ensembl IDs, and local mode with a reference FASTA gene file are shown. (B) Global Tailer-processing (left) uses SAM/BAM-formatted alignment files to infer RNA 3′ ends and post-transcriptional tails based on the SAM CIGAR and GTF annotation files. Local Tailer (right) does not require prealignment of the sequencing data and uses BLAST to align to a user provided FASTA gene database or one generated from provided Ensembl IDs. Local Tailer makes use of reported BLAST metrics of last query mapping position and last reference mapping position to infer tail information. Both modes produce a Tail CSV file with the same columns (bottom). An example output from five reads aligning to the RNU1-1 gene with corresponding SAM-file CIGAR strings is shown.
