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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:

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

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

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
Gene information: tab-delimited file | Excel (.xlsx)

Help us improve the zebrafish transcriptome