Question

Is there any EnsEMBL 90 transcript annotations?

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3 months ago

PK ▴ 130

Hi All,

I was going through a article (Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity) about detecting the spurious splice sites and i got confused about the something. It was mentioned

The remaining reads were aligned against the human genome (version 38, EnsEMBL 90 transcript annotations) using the STAR read aligner (2.5.3a)(Dobin et al., 2013)

Is there any EnsEMBL 90 transcriptome based annotation file?

Can someone help me to understand this?

GTF cgat RNA-Seq • 485 views

ADD COMMENT • link 3 months ago by PK ▴ 130

score 0 · Answer 1 · 2024-08-01

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3 months ago

GenoMax 146k

All Ensembl release 90 files are available in: https://ftp.ensembl.org/pub/release-90/

Human annotation files are in: https://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/

If you are looking for transcript sequence they are here: https://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/cdna/

ADD COMMENT • link 3 months ago by GenoMax 146k

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Please correct me if i'm wrong. The first link you provided for the genome annotation (i could not find transcript based GTF/GFF). Second link also genome. Third is a fasta file. That i have already. What i'm asking is that is there any transcript based GTF/GFF.

ADD REPLY • link 3 months ago by PK ▴ 130

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You will find the transcripts encoded inside the GTF. There will be no transcript based GTF available.

Here is one example

1       havana  gene    11869   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed
_pseudogene";
1       havana  transcript      11869   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX1
1L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "bas
ic"; transcript_support_level "1";
1       havana  exon    11869   12227   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_n
ame "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript";
 exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
1       havana  exon    12613   12721   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_n
ame "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript";
 exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";

ADD REPLY • link 3 months ago by GenoMax 146k

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Thanks for your answer. But please check the sentence that i pasted above. It was mentioned transcript annotation.

ADD REPLY • link 3 months ago by PK ▴ 130

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File above includes transcript annotations. It can be used an in input for STAR analysis during the index generation process.

STAR manual (pages 6-7): https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf