This is the command fixPolishesIID that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
sim4dbutils - utilities to work with sim4db-generated alignment files
convertPolishes - convert between sim4db and GFF3 formats
filterPolishes - filter alignments based on sequence identity, coverage and length.
mergePolishes - merge alignments from multiple files
sortPolishes - sort alignments by cDNA or genomic sequence index or sequence name
convertToExtent - Convert from sim4db format to a single-line tab-delimited format
fixPolishesIID - Updates a sim4db file to use the sequence index of a specific fasta file.
Can also be used to extract a subset of the alignments from the sim4db file.
depthOfPolishes - Outputs a tab-delimited histogram of the depth of polishes at various
headPolishes - print the first N alignments in a file, similar to head(1)
pickBestPolish - report only the 'best' alignment for each cDNA
pickUniquePolish - reports alignments where there is a clear single best alignment for
plotCoverageVsIdentity - Generates (1) a histogram of the percent identity, (2) a
histogram of the percent coverage, and (3) a list of percent identity and coverage (for
use in a scatter plot).
uniqPolishes - Filters out all alignments for cDNA with multiple alignments (-uniq) or
with a single alignment (-dupl). Similar to uniq(1)
realignPolishes - recompute the alignments listed in a sim4db file.
reportAlignmentDifferences - generates a histogram of the types of errors in a set of
alignments Unsupported and Deprecated
comparePolishes - Correlate alignments in two files.
convertToAtac - Converts from sim4db format to ATAC format.
detectChimera - Examines alignments for sequences that might be chimeric.
mappedCoverage - Reports the amount of the query sequence (EST, cDNA) that is covered by
parseSNP - Analyzes alignments for SNPs.
removeDuplicate - searches the input for duplicate alignments.
vennPolishes - Generates a Venn diagram for multiple sim4db files. Used internally by
These programs are a range of utilities to work with sim4db(1)-generated alignment files.
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