error in run

deeksha bhartiya

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Jul 1, 2019, 2:56:56 AM7/1/19

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Hi

I am using Genometricorr for my analysis. I am getting this error

in .permuteIRanges(rd_query[space]$ranges, chr_length) :

The IRanges given for permutation has a range in the that sticks out given chromosome lentgh.

Not sure what to do.

I have tried using configuration file and normal run as well. It is showing this error for both. How should I solve this issue?

I have checked ranges of chromosomes, they seem to fall within range.

Best wishes

Deeksha

Alexander Favorov

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Jul 1, 2019, 2:59:50 AM7/1/19

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Dear Deeksha,
thank you for asking.
The problem could be that the end of one of the intervals in your
query is higher than its chromosome end.
Please test whether it is the cause. If not, please send me the input
and the config file, I will reproduce the issue and do something with
it.

Cheers,
Sasha (AKA Alexander)

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deeksha bhartiya

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Jul 1, 2019, 6:14:12 AM7/1/19

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Dear Sasha

Thanks for your response. Please find the files. Please let me know if you detect the problem. I have just uploaded the query file for one chromosome. For some of the chromosomes the program is working fine. I just want to see if I am missing out anything in this,.

Best Wishes

Deeksha

eg_reference.bed

eg_query.bed

config_genometricorr.ini

deeksha bhartiya

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Jul 1, 2019, 6:35:57 AM7/1/19

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Hi

Also try with the all chromosome file using same config.

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Thanks and Regards

Dr. Deeksha Bhartiya

query_all_chr.bed

deeksha bhartiya

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Jul 26, 2019, 8:15:45 AM7/26/19

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I am still waiting for this response.

Alexander Favorov

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Jul 26, 2019, 8:21:12 AM7/26/19

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Sorry, I was overloaded this time. Thank you for reminding.

On Fri, Jul 26, 2019 at 2:15 PM deeksha bhartiya

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deeksha bhartiya

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Jul 26, 2019, 8:24:50 AM7/26/19

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No problem!

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favorov

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Aug 29, 2019, 3:24:30 PM8/29/19

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Deeksha,

Thank you. Found the bug. The 1.21 will be released very soon.

Still, I recommend preparing the reference a query objects as GRanges with seqinfo that shows the chromosome length (see examples)

Cheers,

Sasha

deeksha bhartiya

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Sep 12, 2019, 9:02:28 AM9/12/19

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Dear Sasha

Thanks a lot!!

Best

Deeksha

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