GENCODE BLAT Track Settings
 
BLAT of GENCODE RNAs   (All Genes tracks)

Display mode:   

Label: alignment Id    gene symbol    gene id    gene type   

Color track by codons or bases: Help on mRNA coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion


Display data as a density graph:
View table schema

Description

BLAT of GENCODE V35 to T2T CHM13 assembly

Methods

Methods are based on those used by the UCSC browser.

  1. Obtained GENCODE RNA sequence from http://gencodegenes.org (gencode.v35.lncRNA_transcripts.fa.gz gencode.v35.pc_transcripts.fa.gz) NCBI.
  2. Aligned to T2t CHM13 using blat -q=rna -fine -minScore=20 -stepSize=5 -noHead.
  3. Filter resulting alignment with pslCDnaFilter -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -globalNearBest=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

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep;22(9):1760-74. PMID: 22955987; PMC: PMC3431492

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. PMID: 16925838; PMC: PMC1810553

A full list of GENCODE publications are available at The GENCODE Project web site.

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