PacBio Iso-Seq, transcript models

Structural annotation/transcript models of RNA (cDNA) sequenced from six different tissues (brain, ileum, lung, ovary, spleen, testis) from the tufted duck on PacBio platform.Full-length non-chimeric (FLNC) reads were built according to PacBio's IsoSeq3 pipeline (ccs, lima, refine), fasta sequences extracted with Bamtools and poly-A tails trimmed with the TAMA tool tama_flnc_polya_cleanup.py. The FLNC reads were mapped to the tufted duck reference genome with Minimap2 and redundant transcript models collapsed with the TAMA tool tama_collapse.py.ccs options: ${--noPolish --minLength=300 --minPasses=1 --minZScore=-999 --maxDropFraction=0.8 --minPredictedAccuracy=0.8 --minSnr=4}lima options: ${--isoseq --dump-clips --no-pbi -j 4 Teloprime.fasta}refine options: ${Teloprime.fasta}Minimap2 options: ${--secondary=no -a -x splice -u f -C 5}tama_collapse.py options: ${-c 95 -x capped -a 100 -z 100}