Lawson Lab zebrafish transcriptome annotation

We have assembled a more comprehensive transcript annotation for zebrafish that includes improved 3' UTR models and genes missing from Ensembl and RefSeq. The files needed to use this annotation for RNA-seq and follow-up analysis are provided below. Gene Transfer Format (.gtf) files comprise exon-, transcript- and gene-level annotation for use in RNA-seq pipelines. We also include gene information files with matching RefSeq, Ensembl, and ZFIN IDs. There are several  annotation versions below. V4.2 and V4.3 are for those interested in replicating analysis from Lawson et al, eLife (2020). V4.3.2 has about 150 gene symbol corrections, but is otherwise the same as 4.3. We recommend that you use the most recent version (V4.3.2).

from eLife manuscript:
V4.2
Genomic annotation file (153.8 MB, md5sum:44c87a2bdd19ccfd9f7cd526f9e21498): V4.2.gtf
Gene information: tab-delimited file | Excel (.xlsx)

V4.3.1
Genomic annotation file (152 MB, md5sum: 19759898187c47edfd9c216162851e31): V4.3.gtf
Gene information: tab-delimited file | Excel (.xlsx)

Updates
V4.3.2 (USE THIS!! as of 8/20/20). As noted above, identical to V4.3.1, except for ~150-200 corrected gene symbols.
Genomic annotation file (152 MB, md5sum: 9ad905ff2ca34971adf58867f7bace99): V4.3.2.gtf (not sorted for cellranger!!, see below)
Gene information: tab-delimited file | Excel (.xlsx)

The following are links to files derived from the V4.3.2 GTF for the purpose of running bulk or single cell RNA-seq pipelines. Thanks to Onur Yukelsen for building these!  

10x Cell Ranger scRNA-seq pipeline: 
Main directory | GRCz11 Fasta (>1GB)|  GTF for v4.3.2 | Commands to create index

Updates for Cell Ranger versions 5 and 6: 
Main directory | GRCz11 Fasta (>1GB)|  sorted GTF for v4.3.2 | Commands

Bulk RNA-Seq using STAR and RSEM
STAR or RSEM Indices for v4.3.2