Comments (1)
Hi @ZachLW - sorry for the confusion. The two polyA mean different things here.
In isoseq refine
, the --require-polyA
means it will remove polyA tails (stretches of A) at the 3' end of the FL read. So after isoseq refine, the reads (now called FLNC reads) will be stripped of 5' / 3' cDNA primers and the polyA tail and just be the transcript insert itself.
In pigeon classify
, the --poly-a
is actually looking for polyadenylation signal that is a 6-mer in the genomic region right upstream of the 3' end of a mRNA transcript. This is the paper that best describes it: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310884/
The common human 6-mer polyA list is here:
https://downloads.pacbcloud.com/public/dataset/Kinnex-single-cell-RNA/REF-pigeon_ref_sets/Human_hg38_Gencode_v39/polyA.list.txt
Hope this helps!
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