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junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
GNU General Public License v3.0
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Change the order of Databases #3

Closed ConYel closed 5 years ago

ConYel commented 5 years ago

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

Non-coding RNA fragments account for the majority of annotated piRNAs expressed in somatic non-gonadal tissues

but I would like to have the option for that.

junchaoshi commented 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.

ConYel commented 5 years ago

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.

junchaoshi commented 5 years ago

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.

ConYel commented 5 years ago

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

junchaoshi commented 5 years ago

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.

ConYel commented 5 years ago

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.

junchaoshi commented 5 years ago

Good point! The link is here: https://ncrnainfo-my.sharepoint.com/:f:/g/personal/sports_ncrna_info/EvZP50IfGFRJlNJwZRujI00BM-CP_w7gITsv8iU45m1rxQ?e=Pk89b9.

ConYel commented 5 years ago

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.

junchaoshi commented 5 years ago

all the database are generated by bowtie1.0 so you can easily customize the database by youself.

ConYel commented 5 years ago

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

junchaoshi commented 5 years ago

gtrnadb only provided hg19 trna database for now.

ConYel commented 5 years ago

Isn't this one for hg38? http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Hsapi38/

junchaoshi commented 5 years ago

good to know, it doesn't show in the homepage.