---
name: "mappedCoverage"
section: "1"
platform: "linux"
package: "sim4db"
version: "0~20150903+r2013-9+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mappedCoverage"
---

# mappedCoverage(1)

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

## 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)](/head/1.md)\
 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)](/uniq/1.md)\
 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)](/sim4db/1.md)-generated alignment files.

## SEE ALSO

[**sim4db**(1)](/sim4db/1.md),\
 http://kmer.sourceforge.net/wiki/index.php/Sim4db\_Files