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Quantifies distinct unique molecular identifiers (UMIs) from a bam file, and performs deduplication in scRNA-seq or targeted sequencing data.

Version 1.0
Bundle sequencing
Authors Kaiyang Zhang (kaiyang.zhang@helsinki.fi)
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Requires libpq-dev (DEB) ; libboost-dev (DEB) ; cython ; pysam ; pandas ; numpy ; future ; umi_tools ; installer (bash)
Source files component.xml main.sh
Usage Example with default values


Name Type Mandatory Description
alignment BAM Mandatory Sorted alignment file, with the index file in the same folder.
annotation GTF Mandatory GTF file defining genes and exons. Make sure the contig names ("1","2", etc or "chr1","chr2", etc) are the same as those in BAM.


Name Type Description
folder BinaryFile All files produced by the tools.
rmdupAlignment BAM Aligned reads after remove duplicates in sorted bam format
table CSV Gene level or exon level UMIcounts.
corrected CSV Gene level or exon level UMIcounts corrected for collision probabilty.


Name Type Default Description
UMIlen int 6 The length of unique molecular identifiers (UMIs).
dedupParams string "--method=adjacency --edit-distance-threshold=1" Define parameters to be used with dedup in UMItools, avaliable methods are "unique", "percentile", "cluster", "adjacency", "directional-adjacency". For more information: https://github.com/CGATOxford/UMI-tools/blob/master/dedup.py. Do not include any that requiere an input file defined above.
featureCountsParams string "-F GTF -R -s 1 --read2pos 5" Define parameters to be used with featureCounts, do not include any that requiere an input file defined above.
picard string "/opt/share/picard/picard.jar" Path to Picard directory, e.g. "/opt/picard", which containg the Picard-tools .jar files. If empty, "/opt/share/picard/picard.jar" will be used, PICARD_HOME environment variable is assumed to point to the Picard directory.
sampleID string (no default) Identifier for the sample (well for single cell experiments); useful when joining statistics tables from different samples or wells

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