Lawson Lab zebrafish transcriptome annotation

We have assembled a 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. Links to the current version that we use (V4.3.2) are provided below. For more information see Lawson et al, eLife (2020). All earlier versions have been deprecated. If you would like them to reproduce the findings in our paper, please let us know.

Lawson Lab Transcriptome Annotation, V4.3.2 
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:
Cell Ranger version 3.
Main directory | GRCz11 Fasta (>1GB; right-click to download)|  GTF for v4.3.2 | Commands to create index

Cell Ranger versions 5 and 6: 
Main directory | GRCz11 Fasta (>1GB; right-click to download)|  sorted GTF for v4.3.2 | Commands

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