Import output from Whippet into Psichomics

[hegu2692]

Hello, I used Whippet to generate files contains Gene, Node, Coord, Strand, Type, Psi, CI_Width, CI_Lo, Hi, Total_Reads, Complexity, Entropy, Inc_Paths, Exc_Paths, Edges (https://github.com/timbitz/Whippet.jl). Can you teach me how to prepare the input file from it so I can continue the downstream analysis? Thanks.

[nuno-agostinho]

Dear @hegu2692, this is now possible to do with the new update: psichomics 1.14.2.

You will have to prepare a tab-separated values (TSV) file where the first column is named AS Event ID. This column must contain unique IDs. In the case of Whippet, I suggest to concatenate the information on the first five columns (Gene, Node, Coord, Strand and Type), e.g. NFIA 2 chr1:61547534-61547719 + AF.

The following columns of the table should contain PSI values (or NA) for each sample. Example:

AS Event ID	SAMPLE-01	SAMPLE-02	SAMPLE-03
NFIA 2 chr1:61547534-61547719 + AF	0.782	NA	0.655
NFIA 4 chr1:61548433-61548490 + CE	0.231	0.122	0.243
TSTX 5 chr6:28845773-28845789 - RI	NA	0.982	0.564
PLLM 3 chr4:47364758-47364824 - CE	0.532	0.453	0.364

You can check my tutorial on how to prepare data for psichomics, including sample metadata and gene expression tables.

I am planning a future update that automatically prepares Whippet output to be loaded in psichomics, but it may take a while to be ready. If you have any further questions, feel free to contact me. Cheers!

[hegu2692]

Dear Nuno Agostinho，   Thank you for your reply. Good luck. Regards, Jian Zhang

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------------------&nbsp;Original message&nbsp;------------------ From: "Nuno Agostinho"; Sendtime: Wednesday, Aug 12, 2020 4:54 PM To: "nuno-agostinho/psichomics"; Cc: "春蚕"<592150634@qq.com>; "Mention"; Subject: Re: [nuno-agostinho/psichomics] Import output from Whippet into Psichomics (#405) Dear @hegu2692, this is now possible to do with the new update: psichomics 1.14.2. You will have to prepare a tab-separated values (TSV) file where the first column is named AS Event ID. This column must contain unique IDs. In the case of Whippet, I suggest to concatenate the information on the first five columns (Gene, Node, Coord, Strand and Type), e.g. NFIA 2 chr1:61547534-61547719 + AF. The following columns of the table should contain PSI values (or NA) for each sample. Example: AS Event ID SAMPLE-01 SAMPLE-02 SAMPLE-03 NFIA 2 chr1:61547534-61547719 + AF 0.782 NA 0.655 NFIA 4 chr1:61548433-61548490 + CE 0.231 0.122 0.243 TSTX 5 chr6:28845773-28845789 - RI NA 0.982 0.564 PLLM 3 chr4:47364758-47364824 - CE 0.532 0.453 0.364 You can check my tutorial on how to prepare data for psichomics, including sample metadata and gene expression tables. I am planning a future update that automatically prepares Whippet output to be loaded in psichomics, but it may take a while to be ready. If you have any further questions, feel free to contact me. Cheers! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.