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Update README.md

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commit 927286012ebb2c4207c5465f15f725bc58058020 1 parent b5743f1
@IgnatiusPang IgnatiusPang authored
Showing with 8 additions and 8 deletions.
  1. +8 −8 README.md
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16 README.md
@@ -22,20 +22,20 @@ Converts a search result from the Mascot protein search engine (or compatible)
into SAM format, so it can be displayed in a genomics viewer.
$ java -jar dist/samifier.jar
- usage: samifier [-b <bedFile>] -c <chromosomeDir> -g <genomeFile> [-l
- <logFile>] -m <mappingFile> -o <outputFile> -r <searchResultsFile>
+ usage: samifier -r <searchResultsFile> -c <chromosomeDir> -g <genomeFile>
+ -m <mappingFile> -o <outputFile> [-l <logFile>] [-b <bedFile>]
[-s <Confidence Score thresold>]
- -b <bedFile> Filename to write IGV regions of
- interest (BED) file to
+ -r <searchResultsFile> Mascot search results file in txt format
-c <chromosomeDir> Directory containing the chromosome
files in FASTA format for the given
genome
+ -m <mappingFile> File mapping protein identifier to
+ ordered locus name
-g <genomeFile> Genome file in gff format
+ -o <outputFile> Filename to write the SAM format file to
-l <logFile> Filename to write the log into
- -m <mappingFile> File mapping protein identifier to
- ordered locus name
- -o <outputFile> Filename to write the SAM format file to
- -r <searchResultsFile> Mascot search results file in txt format
+ -b <bedFile> Filename to write IGV regions of
+ interest (BED) file to
-s <Confidence Score thresold> Minimum confidence score for peptides to
be included
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