Wrong file on annotations download site
Closed this issue · 2 comments
jzluo commented
In https://spliceailookup-api.broadinstitute.org/annotations,
gencode.v44.basic.annotation.txt.gz
is just a compressed gencode.v44.basic.annotation.transcript_annotations.json
.
bw2 commented
I don't understand the issue.
The file contents of gencode.v44.basic.annotation.txt.gz
and gencode.v44.basic.annotation.transcript_annotations.json
are quite different:
$ curl -s https://spliceailookup-api.broadinstitute.org/annotations/gencode.v44.basic.annotation.transcript_annotations.json | head -n 30
{
"ENST00000000233": {
"g_id": "ENSG00000004059.11",
"g_name": "ARF5",
"t_id": "ENST00000000233.10",
"t_priority": "MS",
"t_refseq_ids": [
"NM_001662.4"
],
"t_strand": "+",
"t_type": "protein_coding"
},
"ENST00000000412": {
"g_id": "ENSG00000003056.8",
"g_name": "M6PR",
"t_id": "ENST00000000412.8",
"t_priority": "MS",
"t_refseq_ids": [
"NM_002355.4"
],
"t_strand": "-",
...
and
$ curl -s https://spliceailookup-api.broadinstitute.org/annotations/gencode.v44.basic.annotation.txt.gz | gunzip -c -
#NAME CHROM STRAND TX_START TX_END EXON_START EXON_END
ENST00000456328.2 chr1 + 11868 14409 11868,12612,13220, 12227,12721,14409,
ENST00000450305.2 chr1 + 12009 13670 12009,12178,12612,12974,13220,13452, 12057,12227,12697,13052,13374,13670,
ENST00000488147.1 chr1 - 14403 29570 14403,15004,15795,16606,16857,17232,17605,17914,18267,24737,29533, 14501,15038,15947,16765,17055,17368,17742,18061,18366,24891,29570,
ENST00000619216.1 chr1 - 17368 17436 17368, 17436,
ENST00000473358.1 chr1 + 29553 31097 29553,30563,30975, 30039,30667,31097,
ENST00000607096.1 chr1 + 30365 30503 30365, 30503,
ENST00000417324.1 chr1 - 34553 36081 34553,35276,35720, 35174,35481,36081,
ENST00000606857.1 chr1 + 52472 53312 52472, 53312,
ENST00000642116.1 chr1 + 57597 64116 57597,58699,62915, 57653,58856,64116,
...
jzluo commented
Sorry, I'm not sure what happened. The file I downloaded twice earlier today is different, but redownloading worked just now.
old file:
$ zcat gencode.v44.basic.annotation.txt.gz | head
{
"ENST00000000233": {
"g_id": "ENSG00000004059.11",
"g_name": "ARF5",
"t_id": "ENST00000000233.10",
"t_priority": "MS",
"t_refseq_ids": [
"NM_001662.4"
],
"t_strand": "+",
redownload:
$ zcat gencode.v44.basic.annotation.txt.gz | head
#NAME CHROM STRAND TX_START TX_END EXON_START EXON_END
ENST00000456328.2 chr1 + 11868 14409 11868,12612,13220, 12227,12721,14409,
ENST00000450305.2 chr1 + 12009 13670 12009,12178,12612,12974,13220,13452, 12057,12227,12697,13052,13374,13670,
ENST00000488147.1 chr1 - 14403 29570 14403,15004,15795,16606,16857,17232,17605,17914,18267,24737,29533, 14501,15038,15947,16765,17055,17368,17742,18061,18366,24891,29570,
ENST00000619216.1 chr1 - 17368 17436 17368, 17436,
ENST00000473358.1 chr1 + 29553 31097 29553,30563,30975, 30039,30667,31097,
ENST00000607096.1 chr1 + 30365 30503 30365, 30503,
ENST00000417324.1 chr1 - 34553 36081 34553,35276,35720, 35174,35481,36081,
ENST00000606857.1 chr1 + 52472 53312 52472, 53312,
ENST00000642116.1 chr1 + 57597 64116 57597,58699,62915, 57653,58856,64116,