Description

BLAT of RefSeq currated RNAs (NM_ and NR_) to T2T CHM13 assembly

Methods

Methods are based on those used by the UCSC browser.

  1. Obtained GRCh38 RefSeq RNA dated 2020-05-29 from NCBI.
  2. Aligned to T2t CHM13 using blat -q=rna -fine -minScore=20 -stepSize=5 -noHead.
  3. Estimate Poly(A) lengths with faPolyASizes.
  4. Filter resulting alignment with pslCDnaFilter -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes=<polya> -localNearBest=0.001 -minId=0.92 -minCover=0.75

Display Conventions and Configuration

Data access

Release history

  1. 2020-09-04 t2tChm13_20200727 alignments

Contacts

Credits

O'Leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44(D1):D733-D745. PMID: 26553804 PMCID: PMC4702849, DOI: 10.1093/nar/gkv1189

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.