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Wendellab / homoeologGeneExpression-Coexpression

Challenges and pitfall in the use of partitioned gene counts for homoeologous gene expression and co-expression network analyses
GNU General Public License v3.0
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In silico generation of allopolyploid (AD) datasets #1

Open akcorut opened 3 years ago

akcorut commented 3 years ago

Hi all,

First of all, I would like to say that this is a very helpful and well written paper. I am interested in homoeolog gene expression quantification. And I was trying to use the data mentioned in the paper to reproduce some of the results and also to test some of the stuff I was working on.

In the paper, you mention:

Following adaptor and quality trimming via Sickle [v1.33] [32], the matched A2 and D5 libraries (at each condition and replicate) were adjusted to contain equivalent number of filtered reads and subsequently combined to generate the corresponding in silico allopolyploid (AD) datasets.

However, I wasn't able to track down the in silico allopolyploid datasets you used or the scripts that were used to generate the datasets. I was wondering if it is possible for you to let me know how can I have access those. Sorry that I have missed it if you already mentioned this information in the repo.

Thank you for your time.

Best, Kivanc

huguanjing commented 3 years ago

Hi Kivanc, Thanks for your interest. The in silico dataset was generated from released data PRJNA179447 and PRJNA529417 by concatenating equal sizes of A2 and D5 samples, as described in Methods. Since this procedure is relatively straightforward and the dataset alone is rather large, we didn't depoisit it. Guanjing

akcorut commented 3 years ago

Thanks for the reply @huguanjing. I just wanted to make sure nothing extra has been done to concatenate the A2 and D5 samples. I will use the same approach then.

Thanks again for your time. Kivanc

akcorut commented 3 years ago

I have one last question about the SNP index that was used in the study. I was trying to access the index through several sources but all sources I have tried currently cannot be reached (http://bioinfo3.pgml.uga.edu/polyCat/upload.html or http://cottonevolution.info). Is there any other way to have access the SNP index? I would be glad if you could share that information with me.

Thanks again for your time. Kivanc