IndexError: tuple index out of range about cloops2

[YaqiangCao]

Could you please share some of the test data? I am not sure about the problem based on the current error. Thank you.

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On Fri, Mar 17, 2023 at 2:20 PM poflawless ***@***.***> wrote: Hello Dr/Pro Gao, When I tryied to use the command as below to call domain, cloops2 raised an error: *IndexError: tuple index out of range* cLoops2 callDomains -d Pre_sample1_merge_sampled -o Pre_sample1_merge_sampled_Domain -bs 1000,5000 -ws 500,1000,5000 -p 12, what can I do to correct it? Thanks a lot for your help — Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAOPQKO4IVU3UIUIYSQTUT3W4STN5ANCNFSM6AAAAAAV63ISGI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[poflawless]

Thanks Dr Gao for your reply, please download the file below which I analysed now.

https://filesender.renater.fr/?s=download&token=cb323bc2-a831-4df2-acbc-9dbf7b94246f

Best Wishes,

POFLAWLESS

[YaqiangCao]

Hi POFLAWLESS, Sorry for the late reply. I am quit busy recently. It seems the link is not valid that I can not access the test data. Do you still need the help? Best, Yaqiang

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On Sat, Mar 18, 2023 at 11:03 AM poflawless ***@***.***> wrote: Thanks Dr Gao for your reply, please download the file below which I analysed now. https://filesender.renater.fr/?s=download&token=cb323bc2-a831-4df2-acbc-9dbf7b94246f​ Best Wishes, POFLAWLESS — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAOPQKLNXA24F33MK5U4RXLW4XFF3ANCNFSM6AAAAAAV63ISGI> . You are receiving this because you commented.Message ID: ***@***.***>

[poflawless]

Hello Dr Gao,

Yes, I am need your help urgently. The link will be expired on 4/2, could you please try it again?

https://filesender.renater.fr/?s=download&token=cb323bc2-a831-4df2-acbc-9dbf7b94246f

Best Wishes,
Jing

[YaqiangCao]

Hi JIng, I am downloading the data. What kind of data this is ? Best, Yaqiang

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On Fri, Mar 31, 2023 at 7:11 AM poflawless ***@***.***> wrote: Hello Dr Gao, Yes, I am need your help urgently. The link will be expired on 4/2, could you please try it again? [image: image] <https://user-images.githubusercontent.com/37776318/229104952-eb5653ce-7e95-41a1-8a40-4cedecceaa7d.png> https://filesender.renater.fr/?s=download&token=cb323bc2-a831-4df2-acbc-9dbf7b94246f Best Wishes, Jing — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAOPQKOGYARBKDTUDFKIBNLW623XXANCNFSM6AAAAAAV63ISGI> . You are receiving this because you commented.Message ID: ***@***.***>

[poflawless]

Hello Dr Gao,
I don't really understand your question.
Could you please tell me a little bit more?

Best Wishes,
Jing

[YaqiangCao]

Hi JIng, I mean what kind of data are these? Hi-C? HiChIP? What is the highest resolution? Regarding your parameters "-bs 1000,5000 -ws 500,1000,5000", it may not totally make sense according to my experience of Hi-C or Hi-TrAC data. -bs indicates the bin size for the matrix (resoltuion), and -ws indicates the sliding window size, should be like 5/10/20 folds of the bin size. I have tested your data and if you removed those ctgxxx.ixy and chrC-chrC.ixy, chrM-chrM.ixy, then run "cLoops2 update -d Pre_sample1_merge_sampled", your parameters "cLoops2 callDomains -d Pre_sample1_merge_sampled -o Pre_sample1_merge_sampled_Domain -bs 1000 -ws 5000,10000 -p 12" can be run without problem. What is the expecting size of the called domain if you visualize the data in Juicer or Washu? I would like to suggest using https://github.com/YaqiangCao/cLoops2/blob/master/scripts/getIS.py (calculating insulation score) or https://github.com/YaqiangCao/cLoops2/blob/master/scripts/getSS.py (calculating segregation score as I proposed) to test a small chromosome to optimize the parameters and then run the call Domains. Please also note, the results are highly dependent on your parameters. Best, Yaqiang

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On Fri, Mar 31, 2023 at 12:02 PM poflawless ***@***.***> wrote: Hello Dr Gao, I don't really understand your question. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAOPQKPHH3IHHZXQXTP6DFDW635ZXANCNFSM6AAAAAAV63ISGI> . You are receiving this because you commented.Message ID: ***@***.***>