[ensembl-dev] How transcriptome fasta files are created 2.0

Wed Oct 3 15:38:24 BST 2018

Hi Julien

Apologies for the delay. This might possibly answer your previous and 
current questions.

The split in the gtf file is based on the chromosomal regions. Also 
please note that the “*Homo_sapiens.GRCh38.84.gtf*” file includes all 
the top level chromosomal regions (1..22, X,Y, MT) and also the 
scaffolds, as you can see below.

cut -f1 Homo_sapiens.GRCh38.84.gtf | sort | uniq

1
10
11
12
13
14
15
16
17
18
19
2
20
21
22
3
4
5
6
7
8
9
GL000008.2
GL000009.2
GL000194.1
GL000195.1
GL000205.2
GL000213.1
GL000216.2
GL000218.1
GL000219.1
GL000220.1
GL000224.1
GL000225.1
KI270442.1
KI270706.1
KI270707.1
KI270708.1
KI270711.1
KI270713.1
KI270714.1
KI270721.1
KI270722.1
KI270723.1
KI270724.1
KI270726.1
KI270727.1
KI270728.1
KI270731.1
KI270733.1
KI270734.1
KI270741.1
KI270743.1
KI270744.1
KI270750.1
KI270752.1
MT
X
Y

Also, please note that the '*Homo_sapiens.GRCh38.84.chr.gtf.gz*' 
contains the features only from the primary assemblies

The '*Homo_sapiens.GRCh38.84.chr_patch_hapl_scaff.gtf.gz*' also contains 
the features from haplotypes and patches (for human and mouse only).

More info about haplotype and patches:
https://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html

- The split in the fasta file is based on the *biotype*. So we have 
cdna, cds, ncrna, pep etc., 
(http://ftp.ensemblorg.ebi.ac.uk/pub/release-84/fasta/homo_sapiens/)
If you are interested only in the primary assembly, then he should be 
using the chr.gtf file and ignore any accessions in cdna fasta not in 
gtf as the cdna fasta includes haplotypes.

Hope it helps.

Thanks
Prem

On 03/10/2018 15:07, Julien Wollbrett wrote:
>
> Hello,
>
> As I do not receive answers of my previous email I will try to 
> describe a bit more my goals and questions.
>
> I generated my own transcriptome fasta file using gtf from ensembl, 
> genome fasta file from ensembl (same release) and a tool like 
> gtf_to_fasta (TopHat) or gffread (Cufflinks). Once I did that I 
> compared the generated file with the cdna transcriptome fasta file 
> available at ensembl ftp. Unfortunately I found some differences 
> between my transcriptome fasta file and the one provided by ensembl. 
> That is why I tried to determine the origin of these differences.
> All my tests have been run on different species (human, D. 
> melanogaster, ...) and different releases (84 and 93)
>
> I used the approach described below to define differences :
> - take all transcript_ids from transcriptome fasta file of ensembl
> - take all transcript_ids from gtf file of ensembl
> - detect number of transcript in common in both files and transcript 
> specific to each file
> - map transcript_id to the gtf annotation and detect gene_biotype 
> associated to transcripts of each file.
>
> *results for human release 84:*
>
> gtf file : 
> http://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.gtf.gz
> fasta file : 
> http://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
>
> transcripts common in both files : 161150
> transcripts present only in gtf : 38034
> transcripts present only in fasta file : 15091
> number of different gene biotypes for transcripts present in gtf: 44
> number of different gene biotypes for transcripts in fasta file : 23
> list of biotypes present only in gtf and their count :
>
> gene_biotype  freq
> 3prime_overlapping_ncrna    32
> antisense 10183
> bidirectional_promoter_lncrna     5
> lincRNA 12648
> macro_lncRNA     1
> miRNA  4198
> misc_RNA  2306
> Mt_rRNA     2
> Mt_tRNA    22
> non_coding     3
> processed_transcript  2760
> ribozyme     8
> rRNA   549
> scaRNA    49
> sense_intronic   978
> sense_overlapping   334
> snoRNA   961
> snRNA  1905
> sRNA    20
> TEC  1069
> vaultRNA     1
>
> All the 38034 transcripts present only in gtf have a gene_biotype not 
> present anymore in ensembl transcriptome.
>
> *results for D. melanogaster release 93:*
>
> gtf file : 
> http://ftp.ensembl.org/pub/release-93/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.93.gtf.gz
> fasta file : 
> http://ftp.ensembl.org/pub/release-93/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.cdna.all.fa.gz
>
> transcripts in both files : 30819
> transcripts present only in gtf : 3948
> transcripts present only in fasta : 9
> number of different gene biotypes for transcripts present in gtf: 8
> number of different gene biotypes for transcripts present in fasta 
> file : 2
> list of biotypes present only in gtf and their count :
>
> gene_biotype    freq
> ncRNA    2941
> pre_miRNA    259
> rRNA    115
> snoRNA    289
> snRNA    32
> tRNA    312
>
> All the 3948 transcripts present only in gtf have a gene_biotype not 
> present anymore in ensembl transcriptome.
>
>
> Could someone please explain to me :
>
>     1. Why all the transcripts with these gene biotypes are removed 
> during the creation of the transcriptome ?
>     2. Where do the transcripts present in the transcriptome fasta 
> file but not in the gtf file (15091 in human, 9 in D. melanogaster) 
> come from ?
>     3. How does the cdna transcriptome fasta file is generated ?
>     4. Should I generate my own transcriptome fasta file or take the 
> ensembl cdna fasta file ?
>
> Sorry for such a long email.... and thank you for your answers.
>
> Best Regards,
>
>
> Julien Wollbrett
>
>
>
>
>
>
>
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