SNP calling naive question about instrain HOT 5 OPEN

Hi Nico, I'm a little confused about what you're asking for. If you're looking for the full coverage of every position, you can access that in the raw_data files (e.g. https://instrain.readthedocs.io/en/latest/advanced_use.html#accessing-other-data ) If it's something else you're looking for please let me know Matt — Reply to this email directly, view it on GitHub <#161 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5D6HP5DOUHRR3CFEMEEDX72XBPAVCNFSM6AAAAAA6EBH6TOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONRWG43DSOBWHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

Hi Matt, Sorry if I was confused. Coverage of all positions would work too (covT right?). What I meant initially is that inStrain won't report if there is no variation and basically ref_freq=1. And inStrain won't report if position coverage is null. Just trying to find a way to differentiate both. But maybe it does not make sense... Nico Le mar. 17 oct. 2023 à 12:30, Matt Olm ***@***.***> a écrit : > Hi Nico, > > I'm a little confused about what you're asking for. If you're looking for > the full coverage of every position, you can access that in the raw_data > files (e.g. > https://instrain.readthedocs.io/en/latest/advanced_use.html#accessing-other-data > ) > > If it's something else you're looking for please let me know > > Matt > > — > Reply to this email directly, view it on GitHub > <#161 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABY5D6HP5DOUHRR3CFEMEEDX72XBPAVCNFSM6AAAAAA6EBH6TOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONRWG43DSOBWHE> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> > -- *************************************************************** Nicolas Tromas PhD McGill University E-mail: ***@***.*** ***@***.***> Researchgate: NTromasPage <https://www.researchgate.net/profile/Nicolas_Tromas> Web: http://www.shapirolab.ca/ ***************************************************************

Hi Nico, To load the covT file, you should do something like the following in python: import inStrain import inStain.SNVprofile import inStrain.profile.profile_utilities # Load your inStrain profile IS = inStain.SNVprofile.SNVprofile(`/home/mattolm/inStrainOutputTest/`) # Extract raw covT covT = IS.get('covT') # Declare the scaffold you want to analyze and it's length scaff = 'test_scaffold' scaff_length = 10000 # Get the coverage information for that scaffold scaff_cov = inStrain.profile.profile_utilities.mm_counts_to_counts_shrunk(covT[scaff], fill_zeros=scaff_length) Once you run something like that, scaff_cov will be a python dictionary where if you input a 0-based position it will give you the coverage (e.g. scaff_cov[10]) will report the coverage at position 10 at that scaffold. Best, Matt — Reply to this email directly, view it on GitHub <#161 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABY5D6HJRT6MCHVA7Q3CSQDYCJX6ZAVCNFSM6AAAAAA6EBH6TOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBZGIZTMMJTGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>