Closed ConYel closed 5 years ago
Hi ColYel,
The order cannot be changed yet. As the paper I cited in the history, the exist piRNA database is not good enough and contain a lot of other RNA species. SPORTS1.0 has already optimized the annotation order.
Yes, I know about this issue, but piRBase has been updated to a second version with a lot more sequences. That's is why I wanted to use it before rRNA/tRNA databases.
It's easy to compare the difference: first just annotate miRNA and piRNA and do it again with other databases to see the difference. A lot more sequences don't mean they are good.
I know that this doesn't improve the quality of the sequences, anyway I will use it with and without the other databases. Thank you
No problem. It will be great if you can compare and let me know the difference so that I can consider if it is necessary to put the function in the next version.
Another thing that I would find very useful is if it could the tool have a function that downloads all updated (last versions) databases as in the unitas web tool.
Good point! The link is here: https://ncrnainfo-my.sharepoint.com/:f:/g/personal/sports_ncrna_info/EvZP50IfGFRJlNJwZRujI00BM-CP_w7gITsv8iU45m1rxQ?e=Pk89b9.
Good point! The link is here: https://ncrnainfo-my.sharepoint.com/:f:/g/personal/sports_ncrna_info/EvZP50IfGFRJlNJwZRujI00BM-CP_w7gITsv8iU45m1rxQ?e=Pk89b9.
Are these the latest databases versions? Could you check also the GtRNAdb, you have uploaded the version of hg19-tRNAs with the hg38 genome, so it would be better if you provide the hg38-tRNA version of GtRNAdb.
all the database are generated by bowtie1.0 so you can easily customize the database by youself.
all the database are generated by bowtie1.0 so you can easily customize the database by yourself.
I know about that, I just make a suggestion that would help future users to use the latest versions of databases
gtrnadb only provided hg19 trna database for now.
Isn't this one for hg38? http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Hsapi38/
good to know, it doesn't show in the homepage.
Dear Junchaoshi, Thanks for this great software tool, I would like to know if there is a possibility to change the order of databases annotation. I would like to annotate piRNAdb after miRNA if it is possible. I'm aware of the publication
but I would like to have the option for that.