From 00324f94c25984c9403cb7d0dab916195d08f6a4 Mon Sep 17 00:00:00 2001 From: Philippe Sanio Date: Fri, 27 Sep 2024 11:40:12 -0500 Subject: [PATCH] Fix #35 Update README.md typos and missing information in the README --- README.md | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 9f679a1..d56f8b7 100644 --- a/README.md +++ b/README.md @@ -78,20 +78,23 @@ Optional ## Run Spectre ### MDR file -MDR files hold the information of N regions in the reference genome and restrict Spectre of using data from those regions. +MDR files hold information about N regions in the reference genome and restrict Spectre's use of data from those regions. We are providing sample MDR files for the reference genomes GRCh37 and GRCh38. -If not provided, Spectre will generate a MDR file for you, which can take some time. -Thus, we highly recommend to generate a MDR file for your reference genome before running Spectre on multiple samples which have been aligned to the same reference. +Spectre will generate an MDR file for you if not provided, which can take some time. +Thus, we highly recommend generating an MDR file for your reference genome before running Spectre on multiple samples aligned to the same reference. -Providing an MDR file will save you an substantial amount of time, as Spectre will not have to calculate the N regions for every sample. +Providing an MDR file will save you a substantial amount of time, as Spectre will not have to calculate the N regions for every sample. -Generagtion of MDR file can be with either the `RemoveNs` or `CNVCaller` command. In the latter case, the MDR (metadata.mdr) file will be saved in the output directory of the sample. +The generation of the MDR file can be done with either the `RemoveNs` or `CNVCaller` command. In the latter case, the MDR (metadata. MDR) file will be saved in the sample's output directory. +Running the `RemoveNs` will generate an MDR file under the name in the directory you specified. ```bash spectre RemoveNs \ --reference reference.fasta.gz \ - --output-dir output_directory_path/ + --output-dir output_directory_path/ \ + --output-file name_of_metadata_file.mdr + ``` ### Blacklists The blacklist is a supplementary file to the MDR file. It contains regions which should be ignored by Spectre.