# Seeking Advice on Analyzing Overlap in Taxonomic Classification Results **URL:** \ **Category:** User Support\ **Tags:** feature-classifier, taxonomy\ **Created:** [December 29, 2023, 11:41am UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749 "2023-12-29T11:41:27Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![Antani](https://forum.qiime2.org/user_avatar/forum.qiime2.org/antani/32/11545_2.png) [@Antani](https://forum.qiime2.org/u/Antani)\ **Post date:** [December 29, 2023, 11:41am UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/1 "2023-12-29T11:41:27Z")
Dear QIIME2 Community, I'm currently working on the analysis of my samples where both ITS1 and ITS2 regions have been amplified. I conducted separate analyses for each set of samples. I used the `qiime feature-classifier classify-sklearn` method to classify my representative sequences. Now, I'm interested in understanding the level of taxonomic overlap between the ITS1 and ITS2 sets. Specifically, I would like to know how many sequences have been classified as the same in both datasets. Could you please provide suggestions on how I can obtain this information? Ideally, I would like to generate a list of accession numbers for these shared sequences. Thank you so much for your assistance and any suggestions you can offer. Best, Edo ---
**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [December 29, 2023, 3:28pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/2 "2023-12-29T15:28:06Z")
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**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [December 29, 2023, 7:51pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/3 "2023-12-29T19:51:21Z")
Hi @Antani! So, just to make sure I understand - you used the same taxonomic classifier on two sets of rep seqs? One with the ITS1 region amplified, and the other with ITS2? ---
**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [December 29, 2023, 7:51pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/4 "2023-12-29T19:51:23Z")
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**Author:** ![Antani](https://forum.qiime2.org/user_avatar/forum.qiime2.org/antani/32/11545_2.png) [@Antani](https://forum.qiime2.org/u/Antani)\ **Post date:** [December 29, 2023, 11:37pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/5 "2023-12-29T23:37:46Z")
Hi @lizgehret Correct, same taxonomic classifier on both. I've used the Unite ITS database v9. Thank you so much for your help! ---
**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [January 4, 2024, 5:20pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/6 "2024-01-04T17:20:13Z")
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**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [January 5, 2024, 11:02pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/11 "2024-01-05T23:02:44Z")
Hey @Antani, So sorry for the delayed response here! Unfortunately there isn't an action within QIIME 2 that will accomplish this. I think your best bet would be to try and compare your rep-seqs files in Python or R - returning a list of IDs for all matching values between the two files. Hope this helps! Cheers 🦎 ---
**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [January 5, 2024, 11:02pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/12 "2024-01-05T23:02:47Z")
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**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [January 7, 2024, 10:36pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/14 "2024-01-07T22:36:26Z")
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**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [January 8, 2024, 4:22pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/16 "2024-01-08T16:22:59Z")
Hi @Antani, Just following up on this - there are a couple of options within QIIME 2 that will get you _some_ of what you want (and might get you close enough to what you're wanting without having to write a custom Python/R script). q2-quality-control has the `evaulate taxonomy` action, which compares a pair of observed and expected taxonomic assignments to calculate precision, recall, and F-measure at each taxonomic level, up to maximum level specified by the depth parameter. reSCRIPt also has an action with the same name that will produce a similar output. These actions won't get you a list of IDs, but will provide you with general quantification of the amount of overlap between the two datasets. Hope this helps! Cheers 🦎 ---
**Author:** ![lizgehret](https://forum.qiime2.org/user_avatar/forum.qiime2.org/lizgehret/32/17128_2.png) [@lizgehret](https://forum.qiime2.org/u/lizgehret)\ **Post date:** [January 8, 2024, 4:23pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/17 "2024-01-08T16:23:04Z")
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**Author:** ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Post date:** [January 8, 2024, 5:20pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/18 "2024-01-08T17:20:28Z")
Hi @Antani , See also `qiime rescript evaluate-classifications`. Good luck! ---
**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\ **Post date:** [February 8, 2024, 11:21pm UTC](https://forum.qiime2.org/t/seeking-advice-on-analyzing-overlap-in-taxonomic-classification-results/28749/19 "2024-02-08T23:21:11Z")
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