Instructions for parseBlastXML_calcErrRate.pl
This script parses the xml output file from NCBI's Blastn program and calculates average error rates of different types (insertion, deletion, substitution).
- Blastn output xml file.
- Cutoff value for fraction of query sequence that aligned to subject sequence (0-1). The alignment that fraction is below the cutoff is considered as randomly. The default value is 0.6.
- Stats file of calculated three types of error rates.
- Optional pairwise alignment file of each query aligned to reference and the counts of insertions, deletions and substitutions.
How to run
- Download parseBlastXML_calcErrRate.pl to your local computer, and set it as executable by typing the following command in your working directory:
chmod +x parseBlastXML_calcErrRate.pl
Create a subdirectory in your working directory to hold input files and output files. In the subdirectory, type following command:
perl ../parseBlastXML_calcErrRate.pl blastXmlOutFile outputStatsFile alignFractionCutoff pairwiseAlignFile(optional)