From 22d534a8f7ebae64e1ce8cb1fc9323ce9ec95629 Mon Sep 17 00:00:00 2001 From: Subina Mehta Date: Fri, 13 Oct 2023 15:05:30 -0400 Subject: [PATCH 1/2] Update tutorial.md with new link for fasta file --- .../proteomics/tutorials/proteogenomics-dbcreation/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md index 2eb1b3b85e753f..1d257d51c8d025 100644 --- a/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md @@ -73,7 +73,7 @@ In this tutorial, protein and the total RNA sample was obtained from the early d > > 2. Import the Uniprot FASTA, FASTQ file and the GTF file from Zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1489208.svg)](https://doi.org/10.5281/zenodo.1489208) > ``` -> https://zenodo.org/api/files/bf8c34bc-ed55-4b1c-9b69-edfe0926ea84/Trimmed_ref_5000_uniprot_cRAP.fasta +> https://zenodo.org/records/1489208/files/Trimmed_ref_5000_uniprot_cRAP.fasta > https://zenodo.org/record/1489208/files/FASTQ_ProB_22LIST.fastqsanger > https://zenodo.org/record/1489208/files/Mus_musculus.GRCm38.86.gtf > ``` From 6357204a67e2ba2a197615f68d74ff9002316f2c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 13 Oct 2023 22:00:43 +0200 Subject: [PATCH 2/2] Update tutorial.md --- .../tutorials/proteogenomics-dbcreation/tutorial.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md index 1d257d51c8d025..fc0d464672d7d6 100644 --- a/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md @@ -645,13 +645,10 @@ Generate a list of Reference Proteins. Identify peptides that are contained in t > - All the tools mentioned in this tutorial are subjected to change when the tool version is upgraded . {: .comment} - -# **Conclusion** - +# Conclusion This completes the walkthrough of the proteogenomics database creation workflow. This tutorial is a guide to have a database and mapping files ready for Database searching and novel peptide analysis. Researchers can use this workflow with their data also, please note that the tool parameters, reference genomes and the workflow will be needed to be modified accordingly. This workflow was developed by the Galaxy-P team at the University of Minnesota. For more information about Galaxy-P or our ongoing work, please visit us at [galaxyp.org](https://galaxyp.org) - {: .comment}