get dbsnps_SET_RELEASE.tar.gz issue

[wangxiran0622]

The download link https://bamquery.iric.ca/download/dbsnps_SET_RELEASE.tar.gz is inaccessible or expired. How can I download the specific compressed file?

[wangxiran0622]

The download link https://bamquery.iric.ca/download/snps_mouse_SET_RELEASE.tar.gz is inaccessible or expired. How can I download the specific compressed file?

[wangxiran0622]

For the Genome Versions v26_88, v33_99, and v38_104, the specific files that need to be downloaded vary depending on the version. Here are the specific requirements and file naming conventions for each version

[sebastien-lemieux]

Hello, you need to form the URL by replacing SET_RELEASE by the release version you want. For example: https://bamquery.iric.ca/download/snps_mouse_GRCm39.tar.gz

[wangxiran0622]

Before to continue you must provide all the tissue information for the bam files annotated in the file : ./normal_mode_example/output/res/AUX_files/bam_files_tissues.csv. Please enter for each sample : tissue, tissue_type, shortlist (yes/no).

[wangxiran0622]

I have a question about this kind of error, is the format of the input file incorrect? What format should the correct input file be?Before to continue you must provide all the tissue information for the bam files annotated in the file : ./normal_mode_example/output/res/AUX_files/bam_files_tissues.csv. Please enter for each sample : tissue, tissue_type, shortlist (yes/no).

[wangxiran0622]

File "/home/wangbing/wangxiran/software/anaconda3/envs/BamQuery/bin/BamQuery/readers/read_input.py", line 154, in treatment_file
raise Exception("Sorry, You must provide peptides in the appropriate format mode : peptide/CS/manual ")
Exception: Sorry, You must provide peptides in the appropriate format mode : peptide/CS/manual

[wangxiran0622]

It is good to have a standard test input file when testing software. Can you provide one? This place always reports errors

[VirginieR]

Hi Wang,

Please, refer to this part of the documentation to have more information about how to fill the file : bam_files_tissues.csv

Also, please refer to this part of the documentation for sample inputs and guidance on how to provide input information to run BamQuery.

I hope this helps!