Comments (10)
UTA needs an update. The most recent version is uta_20180821. Although NM_007194.4 is in UTA, the 38 alignment for it is not. This typically means that it wasn't in the gff3 files at the time of the snapshot, or that it failed alignment criteria and was rejected. The criteria were selected with input from Terence M. in an effort to match alignment filtering at NCBI. NM_007194.4 became current on June 13, 2018, so perhaps the alignments didn't exist in Aug 2018.
I am looking for funding to automate the construction of UTA so that it doesn't fall so far behind.
from uta.
Additional comments:
-
UTA does contain the alignment of .3 to 38. So, if you know that that exon structures and alignments are consistent in this exon, you can probably get a way with using .3.
-
You can see available transcripts and alignments like this:
$ export PGPASSWORD=uta_public
$ psql -h uta.biocommons.org -d uta -U uta_public
uta_public@uta/uta=> set search_path = uta_20180821;
uta_public@uta/uta=> select tx_ac,alt_ac,alt_aln_method from exon_set where tx_ac ~'^NM_007194' order by 1,2;
┌─────────────┬──────────────┬────────────────┐
│ tx_ac │ alt_ac │ alt_aln_method │
├─────────────┼──────────────┼────────────────┤
│ NM_007194.3 │ AC_000154.1 │ splign │
│ NM_007194.3 │ NC_000022.10 │ splign │
│ NM_007194.3 │ NC_000022.10 │ blat │
│ NM_007194.3 │ NC_000022.11 │ splign │
│ NM_007194.3 │ NC_018933.2 │ splign │
│ NM_007194.3 │ NG_008150.1 │ splign │
│ NM_007194.3 │ NM_007194.3 │ transcript │
│ NM_007194.4 │ NC_000022.10 │ splign │
│ NM_007194.4 │ NM_007194.4 │ transcript │
└─────────────┴──────────────┴────────────────┘
(9 rows)
from uta.
Hi Reece,
Thanks for the update. It turns out my bigger problem is that I need to project alignments onto NM_001257387.2, which does not seem to be in 37, only .1 is in 37. These two seem a bit different - at least based on length (.1 is 1976 bases and .2 is 1958 bases)
Is there another source I can get the UTA updated from?
Is it difficult to install UTA and then add information to it?
Thanks for your help- I appreciate this is unfunded but it is super valuable. If there is anything I can do to help (letters, etc) please let me know.
best,
-deanna
from uta.
Updating UTA is a pain right now, which is why it's languished (much to my chagrin). I wouldn't wish that process on anyone. (However, instructions do exist if you're feeling intrepid. It refers to hosts within Invitae, but the process would be the same for your own installations.)
As for the offer of help, thanks! I'll follow up by email.
from uta.
Thanks Reece- appreciate the rapid response on the update.
from uta.
Note to self for future UTA update: I had hoped to use the gff3 files as-is for UTA cigar strings. This won't be possible because the gff3 files don't denote mismatches, which hgvs uses to correct for reference sequence differences.
Example:
GCF_000001405.28_knownrefseq_alignments.gff3 (mirrored on 2019-09-05) contains:
NC_000010.11 RefSeq cDNA_match 87863438 87864548 1104.71 + . ID=d73f8942-0138-46b9-8e95-56e7ebc1c240;Target=NM_000314.6 1 1110 +;gap_count=1;identity=0.99977;idty=0.9982;num_ident=8700;num_mismatch=1;pct_coverage=100;pct_identity_gap=99.977;pct_identity_ungap=99.9885;Gap=M666 D1 M444
UTA contains the cigar string M666 I1 39=1X404=
. The I/D swap is because UTA is transcript-centric. The more interesting difference is the 39=1X404=
/ M444
difference. The length is the same, but the uta alignment correctly picked up that there is a mismatch. Note that NCBI's gff3 shows num_mismatch=1
.
The upshot is that UTA will need to continue aligning regions in order to pick up mismatches.
from uta.
This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.
from uta.
This issue was closed because it has been stalled for 7 days with no activity.
from uta.
This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.
from uta.
This issue was closed because it has been stalled for 7 days with no activity.
from uta.
Related Issues (20)
- RFC: Should we migrate to fully-justified alignments? HOT 4
- ncbi-parse-gbff error HOT 1
- ncbi-parse-gff error: HOT 6
- is there difference between uta_20150827 and uta_20180821 in above commands? HOT 1
- why I can not find table uta_20180821.meta ?(docker version) HOT 5
- Refreshing tx_similarity_mv takes several hours HOT 9
- Building from a custom source HOT 4
- 20210129 version not on dockerhub HOT 4
- ENSEMBL transcripts not versioned HOT 7
- Add support for the telomer-to-telomer assembly (T2T) HOT 4
- 1 HOT 2
- Workflow for adding updated refseq alignment data HOT 4
- Unable to use the uta_20210129 locally or in docker HOT 8
- solved HOT 2
- Documentation for installing UTA locally on Mac HOT 4
- Consider standardized schema for transcripts HOT 3
- Cannot connect to DB (and a variant question) HOT 7
- GHA for automating UTA HOT 1
- sqlite support? HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from uta.