From 049f86eba3e7183830850c010d5ae7505e1d2b5e Mon Sep 17 00:00:00 2001 From: Fengchao Date: Sun, 17 Dec 2023 14:11:21 -0500 Subject: [PATCH] Add the group FDR tutorial. --- docs/tutorial_group_fdr.md | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 docs/tutorial_group_fdr.md diff --git a/docs/tutorial_group_fdr.md b/docs/tutorial_group_fdr.md new file mode 100644 index 000000000..6f2ec8eff --- /dev/null +++ b/docs/tutorial_group_fdr.md @@ -0,0 +1,33 @@ +## Perform group FDR estimation for different identification groups + +##### [FragPipe](https://fragpipe.nesvilab.org) can be downloaded [here](https://github.com/Nesvilab/FragPipe/releases). Follow the instructions on that same Releases page to launch the program. See [here](https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html#configure-fragpipe) for help configuring FragPipe. + +FragPipe can perform a group FDR estimation to calculate FDRs for each group separately. Then groups can be the number of enzymatic termini (_i.e._ 0, 1, 2) and the protein evidence levels encoded in the FASTA file. + +The group FDR approach supports most workflows. After loading a specific workflow, go to the MSFragger tab to select the group type. + +![](https://raw.githubusercontent.com/Nesvilab/FragPipe/gh-pages/images/group_fdr_1.png) + +Then, go to the `Validation` tab, and add `--group` to the `FDR Filter and Report` command box + +![](https://raw.githubusercontent.com/Nesvilab/FragPipe/gh-pages/images/group_fdr_2.png) + +The rest of the part is the same as that in a normal FragPipe analysis. + +To make FragPipe recognize the encoded protein evidence, the protein header in the FASTA file must have the `PE=` keyword. The numbers after `PE=` identify different groups. [Here](https://github.com/bassanilab/CircRNA_MS_ref_fasta) has a handy script to revise the protein headers. + + + +
+
+ + +#### Key References +_coming soon_ + + + +
+
+ +#### [Back to FragPipe homepage](https://fragpipe.nesvilab.org/)