xenial (1) filterPolishes.1.gz

Provided by: sim4db_0~20150903+r2013-1_amd64 bug

NAME
       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 window sizes.
       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 each cDNA.
       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 alignments.
       parseSNP - Analyzes alignments for SNPs.
       removeDuplicate - searches the input for duplicate alignments.
       vennPolishes  -  Generates  a  Venn  diagram  for  multiple  sim4db  files.  Used internally by ESTMapper
       cleanPolishes
       summarizePolishes


DESCRIPTION
       These programs are a range of utilities to work with sim4db(1)-generated alignment files.


SEE ALSO
       sim4db(1),
       http://kmer.sourceforge.net/wiki/index.php/Sim4db_Files

                                                  January 2016                                    SIM4DBUTILS(1)