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Issues about Diff_APA_site_analysis #13

Open maximumko opened 4 years ago

maximumko commented 4 years ago

Hello! I'm trying to detect APA sites of TCGA samples via TAPAS. I followed this protocol<Step1, APA site detection; Step2, Diff_APA_site_analysis; Step3...> The problem came out when I run the Step2: Diff_APA_site_analysis. Here's my code:

./Diff_APA_site_analysis -C1 ./expression.txt -C2 ./expression_normal.txt -a ./refFlat_sf.txt -cutoff 70 -type s -o /data/TAPAS/output.txt

And here's the bug information: No input file with name diff_result.txt No input file with name diff_result_for_sl.txt rm: cannot remove `diff_result_for_sl.txt': No such file or directory

I have checked all the necessary files and tried to run it for your sample files while it still not works.

./Diff_APA_site_analysis -C1 /data/biosoft/TAPAS-master/sample/expression_with_cp_chrX.txt -C2 /data/biosoft/TAPAS-master/sample/expression_with_cp_chrY.txt -a ./refFlat_sf.txt -cutoff 70 -type s -o /data/TAPAS/output.txt No input file with name diff_result.txt No input file with name diff_result_for_sl.txt rm: cannot remove `diff_result_for_sl.txt': No such file or directory

Any idea what is missing?

Best regards Ray

arefeen commented 4 years ago

Hi Ray,

Thanks a lot for using TAPAS and I am extremely sorry for not replying to your question in time. I have few suggestions to overcome the error:

  1. Try to keep all the files in one directory.
  2. The differential and shortening/lengthening analyses are designed for multiple replicates of two samples. Therefore, please use multiple replicates while running step2 and 3.

Please let me known if you have any question or concern.

Thanks Ashraful

maximumko commented 4 years ago

Hi Ray,

Thanks a lot for using TAPAS and I am extremely sorry for not replying to your question in time. I have few suggestions to overcome the error:

  1. Try to keep all the files in one directory.
  2. The differential and shortening/lengthening analyses are designed for multiple replicates of two samples. Therefore, please use multiple replicates while running step2 and 3.

Please let me known if you have any question or concern.

Thanks Ashraful

Dear Ashraful! Thank you for your kindness and advice. I've tried to keep all the files in one directory and still failed to run with multiple replicates of two samples. I still cannot figure out the reason... Best wishes! Ray

arefeen commented 4 years ago

Hi Ray, Sorry for the late reply.

Can you please share your scripts? How many replicates you are using? Moreover, can you please share the issue log?

You can also email me detailed information of your experiment.

Thanks, Ashraful

SheetalTMU commented 1 year ago

Hello Ma'am,

I want to find out isoforms through RNA-seq data. I am facing a problem in creating 'refFlat_sf.txt'. I have a .gtf file for reference, but this file format is different from the .gtf file. If you can let me know how to create this file, that would be really helpful.

Thank you so much for your time.

Lei-Guo commented 1 year ago

I'm having the same problem. Any solutions?

OK, I got it. You have to copy all the scripts from the "Differential_APA_Site_Analysis" folder to your data folder.

arefeen commented 1 year ago

Hi, Please Google to convert gtf file to refflat.txt file format.

On Tue, Feb 14, 2023, 8:35 AM Lei-Guo @.***> wrote:

I'm having the same problem. Any solutions?

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