Qingqing Wang

Hi Linda, Would you send me the first 50 lines of your refFlat annotation file? Qingqing On Tue, May 5, 2020 at 1:56 PM Linda Lin wrote: > Hello, >...

If you don't mind, could you send me the input files and the command you used to run JUM_C.sh? I suspect it is some format issue in the input files...

Sorry for the late reply - was swamped the last two weeks. The reason you were seeing this error is because when you ran JUM previously all the chromosome names...

Do you mind giving me an example of the "none" IRs that you described as "I inspected these visually and it appears that approximately half are annotated as exons/UTRs rather...

Yes this error was caused by not installed the corresponding modules on user end. Please see the manual on "installation": Requirements: Perl (5+) with modules Array::Utils and Statistics::Descriptive (for checking...

I apologize for the late reply. You can not just add another column to the design matrix to include batch effect. If you want to analyze the influence of batch...

Hi Andrew, So I noticed one thing in your command: the original command bash /user/home/JUM_2.0.2/JUM_B.sh --Folder /user/home/JUM_2.0.2/JUM_diff --Test pvalue --Cutoff 0.05 --TotalFileNum 6 --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2 --Condition1SampleName ctrl1,ctrl2,ctrl3 --Condition2SampleName...

Did you sort your input bam files accordingly to the manual? Convert and sort the resulted alignment files (please use the exact naming nomenclature as shown below). Here we show...

Yes you set the p-value cutoff to different values and JUM results will be filtered differently according to your setting. So you will see different results. A p-value at 1...

if you first run JUM with padj_1, you should be able to retrieve the exact same results by filtering the raw results using any new threshold values v.s. running JUM...