tRNAdecoder

Isodecoder level analysis for Nano-tRNAseq runs.

Installation

pip install tRNAdecoder

Running it

align

It accepts both, FastQ (can be gzippped) and SAM/BAM/CRAM files. If SAM/BAM/CRAM is provided, it'll output all tags.

It outputs sorted BAM. Unmapped reads are not reported.

s=sacCer3
ref=/no_backup/enovoa/reference_fasta/app/v1.1/$s.fa.gz
for f in /no_backup/enovoa/data/app/1.1/Laia_tRNA_sacCer3_rna004_fast_b13_10/AV_yeast_RAPPL_pilot/RNA260326_total/reads.bc_*.bam; do
    bc=$(basename $f|cut -f2 -d'.')
    runid=$(basename $(dirname $f))
    echo `date` $runid $bc
    tRNAdecoder align -v -f $ref -i $f -o test/$s/$runid/$bc.bam
done; date