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| author | Hui Lan <lanhui@zjnu.edu.cn> | 2022-10-09 15:17:41 +0800 |
|---|---|---|
| committer | Hui Lan <lanhui@zjnu.edu.cn> | 2022-10-09 15:17:41 +0800 |
| commit | 0cc41d5838c887bb3f3f272b37abd8220d9d521a (patch) | |
| tree | e8bbf7fee42ae55bfb521ea9c11b2233b81e371b | |
| parent | efb889c19119acc62c7000d371c123bac43e8344 (diff) | |
QUICKSTART.rst: exchange two paragraphs.
| -rw-r--r-- | brain.documentation/QUICKSTART.rst | 6 |
1 files changed, 3 insertions, 3 deletions
diff --git a/brain.documentation/QUICKSTART.rst b/brain.documentation/QUICKSTART.rst index 7025c09..c177377 100644 --- a/brain.documentation/QUICKSTART.rst +++ b/brain.documentation/QUICKSTART.rst @@ -114,16 +114,16 @@ The user manually updates paramter_for_buildCmatrix.txt. (Automatic updating is Other mandatory files to prepare
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-In the above three parameter files, the user needs to specify paths to certain files, e.g., GENE_LIST, GENE_ID_AND_GENE_NAME and GENE_FILE.
+In the above three parameter files, the user needs to specify paths to certain files, e.g., GENE_LIST, GENE_FILE, GENE_ID_AND_GENE_NAME, etc.
- **GENE_LIST.** Each line contains one gene ID. The gene ID should not contain isoforms. For example, use AT1G01020 but not AT1G01020.1 or AT1G01020.2. Example: *Data/information/gene-list.txt* contains a list of AGI IDs, one for each line. Only these IDs will be used when building the regulatory network. This file is used both in parameter_for_net.txt and in parameter_for_buildRmatrix.txt.
-- **GENE_ID_AND_GENE_NAME.** Each line contains one gene ID and one gene name. If a gene has multiple names, separate them by semicolons. Example: the file *Data/information/AGI-to-gene-names_v2.txt* has two columns. The left column is AGI, and the right column is gene names (separated by semicolons). This file is used in many places where a gene name is needed, for example, in create_edges4.py.
-
- **GENE_FILE.** Each line contains a gene ID, gene name, gene position, gene orientation and gene annotation (optional). See gene_file_. Example: *Data/information/gene_file.txt*. This file is used to help convert a narrowPeak file into a binding file. An example file is available at gene_file.txt.gz_
.. _gene_file.txt.gz: http://118.25.96.118/brain/static/info/gene_file.txt.gz
+
+- **GENE_ID_AND_GENE_NAME.** Each line contains one gene ID and one gene name. If a gene has multiple names, separate them by semicolons. Example: the file *Data/information/AGI-to-gene-names_v2.txt* has two columns. The left column is AGI, and the right column is gene names (separated by semicolons). This file is used in many places where a gene name is needed, for example, in create_edges4.py.
- **rnaseq_info_database.json** -- this file must be put under *Data/information*. All experimental conditions for RNA-seq samples are contained in this file. This file should be updated quarterly. For how to make this file, see rnaseq.info.database_.
|