low sensitibity using local search mode

[yye88]

Hello, thank you for previous helps. The search went great in NCBI BLAST API. Then I tried the local database, but found that the sensitivity is quite low. I am sure my local genome library has at least ten clusters containing both gene_a and gene_b, but the search returned me zero hit. I adjusted the –min_identity argument, but made no difference. Would you please tell me how to increase the sensitivity of the local search mode? Thank you.

[gamcil]

Hi, most of the time this is the result of the clustering arguments - could you try lowering the --min_hits and --unique arguments? By default, they are set to 3, so clusters containing less than 3 unique hits are discarded.

For the actual sequence search sensititivity, I'll be adding an argument for controlling the sensitivity of DIAMOND in the next update.

[yye88]

Thank you very much for the suggestion and future update!

[gamcil]

Closing this issue as you can now adjust the DIAMOND sensitivity as of v1.3.12 (https://github.com/gamcil/cblaster/releases/tag/v1.3.12).

[yye88]

Thank you very much!

…

On Mon, Dec 13, 2021 at 11:55 AM Cameron Gilchrist ***@***.***> wrote: Closing this issue as you can now adjust the DIAMOND sensitivity as of v1.3.12 (https://github.com/gamcil/cblaster/releases/tag/v1.3.12). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#68 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWKR2WKTJG6B5NYJUQWZUULUQVVE7ANCNFSM5HXIGVBQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.