Annotate gene symbol and exon number

[komalsrathi]

Hi,

I wanted to know if there is any way to annotate gene_name and exon_number in addition to the transcript_id from the GTF file:

GTF file:

##description: evidence-based annotation of the human genome (GRCh37), version 19 (Ensembl 74)
##provider: GENCODE
##contact: [email protected]
##format: gtf
##date: 2013-12-05
##modified by GTEx_Collapsed_Gene_Model.py
1       HAVANA  gene    11869   14362   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_s
tatus "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG000000009
61.2";
1       HAVANA  transcript      11869   14362   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"
; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG0
0000000961.2";
1       HAVANA  exon    11869   12227   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_s
tatus "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG000000009
61.2"; exon_id "ENSG00000223972.4_1; exon_number 1";
1       HAVANA  exon    12595   12721   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_s
tatus "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG000000009
61.2"; exon_id "ENSG00000223972.4_2; exon_number 2";
1       HAVANA  exon    12975   13052   .       +       .       gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_s
tatus "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG000000009
61.2"; exon_id "ENSG00000223972.4_3; exon_number 3";

Sashimi Plot:

Thanks
Komal

[dgarrimar]

Hi @komalsrathi, currently it is not possible with ggsashimi to annotate the gene name/exon number, but we will take into account your suggestion for future developments. Thanks!

[PedroBarbosa]

I would like to reopen this issue just to highlight how useful and important this feature would be.

Best,
Pedro

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[luxeredias]

I had a similar demand. I needed to show the "transcript_name" instead of "ensembl_transcript_id" from each transcript in the GTF plot. What I did was alter lines 291 and 293 of the original code from:

"try:
transcript_id = re.findall('transcript_id ("[^"]+")', tags)[0]
except KeyError:
print("ERROR: 'transcript_id' attribute is missing in the GTF file.")
exit(1)
"

to:

"try:
transcript_id = re.findall('transcript_name ("[^"]+")', tags)[0]
except KeyError:
print("ERROR: 'transcript_name' attribute is missing in the GTF file.")
exit(1)
"

Maybe if you do the same you'll have at least an indication of the gene you are plotting without the need to add anything else to the plot later!

[dgarrimar]

Thanks @luxeredias, that is indeed a possibility for alternative transcript names. With respect to gene names, as pointed out originally by @komalsrathi and @PedroBarbosa, the point is where to add the gene name. For instance, when plotting a region that contains several genes it can be difficult to place the gene label in the right place. Suggestions and PR's are wellcome! As for exon numbers, I think they could be added relatively straigthforward if users are interested.

[bdgsilva]

Hi @dgarrimar,
I just wanted to say I would be super interested in having exon numbers in the annotation as well. I think it would be a great addition, not least because no other tools offer that feature so far, to the best of my knowledge