Questions about the new norm v3 features from the new BioRxiv paper

[JasminGao]

Hello authors,

In your newest paper on BioRxiv, Selection scans and downstream analysis with selscan, you mentioned that some new features in norm can directly assign window scores to genes and regress the scores onto gene length, which I am very keen to try out. However, when I ran the norm program with this command: ./norm --nsl --annotate-win *1000kb.windows --gene-bed all_protein_genes_38.bed, I recieved an error:
norm v1.3.1 ERROR: command line flag --annotate-win not recognized. ERROR: command line flag *1000kb.windows not recognized. ERROR: command line flag --gene-bed not recognized. ERROR: command line flag all_protein_genes_38.bed not recognized.
Is it because the new version is still not available, or I wasn't using the newest version?

Many thanks!

Best wishes,
Jasmin

[szpiech]

Hi Jasmin, Currently v3.0 is not yet pushed to the main branch. You can access this version on the release_v3 branch ( https://github.com/szpiech/selscan/tree/release_v3). This branch will be updated with a few final changes as we revise our manuscript and will be pushed to main shortly after (likely within a month), but you can start using it now if desired. One thing to know is that in v3.0 we have combined the norm program into selscan, and there will be only one binary to use moving forward. So, whereas you would previously run ./norm ..., you will now run ./selscan norm ... to access norm features. Currently, selscan norm's gene annotation and length regression feature functions only on individual chromosomes, and you will need to separate your gene bed file accordingly to run for each chromosome separately. We realize this is a less than desirable set up, so we will be updating the code to allow for analyzing all chromosomes and genes at once, but right now you'll have to split them. Hope this helps, Zachary

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On Sun, Nov 16, 2025 at 9:38 PM JasminGao ***@***.***> wrote: *JasminGao* created an issue (szpiech/selscan#151) <#151> Hello authors, In your newest paper on BioRxiv, Selection scans and downstream analysis with selscan, you mentioned that some new features in norm can directly assign window scores to genes and regress the scores onto gene length, which I am very keen to try out. However, when I ran the norm program with this command: ./norm --nsl --annotate-win *1000kb.windows --gene-bed all_protein_genes_38.bed, I recieved an error: norm v1.3.1 ERROR: command line flag --annotate-win not recognized. ERROR: command line flag *1000kb.windows not recognized. ERROR: command line flag --gene-bed not recognized. ERROR: command line flag all_protein_genes_38.bed not recognized. Is it because the new version is still not available, or I wasn't using the newest version? Many thanks! Best wishes, Jasmin — Reply to this email directly, view it on GitHub <#151>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABAKRQSLTXAFMRWEJH5DPLD35EYJXAVCNFSM6AAAAACMJE46JKVHI2DSMVQWIX3LMV43ASLTON2WKOZTGYZTCNBZG43DONQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[JasminGao]

Hi Zachary,

Thank you so much, I appreciate the timely reply! I'll separate my bed file and try running the new functions.

Best wishes,
Jasmin