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Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 14 Jan 2017 11:50:59 +0100
Description: Adapt usage hint to how it is used on Debian
--- a/README.txt
+++ b/README.txt
@@ -44,7 +44,7 @@ Unzipping ArtificialFastqGenerator.zip w
ArtificialFastqGenerator can be run with any reference sequence in FASTA format. Below is information about all of its user
parameters:
-usage java -jar ArtificialFastqGenerator.jar -O <outputPath> -R <referenceGenomePath> -S <startSequenceIdentifier>
+usage: artificialfastqgenerator -O <outputPath> -R <referenceGenomePath> -S <startSequenceIdentifier>
-F1 <fastq1ForQualityScores> -F2 <fast2ForQualityScores> -CMGCS <coverageMeanGCcontentSpread> -CMP <coverageMeanPeak>
-CMPGC <coverageMeanPeakGCcontent> -CSD <coverageSD> -E <endSequenceIdentifier> -GCC <GCcontentBasedCoverage>
-GCR <GCcontentRegionSize> -L <logRegionStats> -N <nucleobaseBufferSize> -OF <outputFormat> -RCNF <readsContainingNfilter>
@@ -84,7 +84,7 @@ accepting Phred quality scores from test
should include the file base name (e.g. $OUTPUT_DIR/Chr1), and the -S and -E parameters are prefixes of the desired sequence
identifiers, sufficiently long to ensure a match.
-java -jar ArtificialFastqGenerator.jar -R miniReference.fasta -O C1 -S ">1" -E ">" -URQS true -SE true -F1 test1.fastq -F2 test2.fastq
+ artificialfastqgenerator -R miniReference.fasta -O C1 -S ">1" -E ">" -URQS true -SE true -F1 test1.fastq -F2 test2.fastq
Apart from the artificial FASTQs, ArtificialFastqGenerator will output a file which contains the start and end indexes in the
reference sequence of all the generated reads, and a log file which contains the parameter settings and summary coverage and
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