Description

IsoSeq3 - Cluster - Cluster trimmed consensus sequences

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test' ]

bam (file)

BAM file generated by isoseq3 refine

*.bam

Output

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

version (file)

File containing software version

versions.yml

bam (file)

BAM file of clustered consensus

*.transcripts.bam

pbi (file)

Pacbio Index of consensus reads generated by clustering

*.transcripts.bam.pbi

cluster (file)

A two columns (from, to) file describing original read name to new read name

*.transcripts.cluster

cluster_report (file)

A table files clusters (transcripts) members (read)

*.transcripts.cluster_report.csv

transcriptset (file)

A metadata xml file which contains full paths to data files

*.transcripts.transcriptset.xml

hq_bam (file)

High quality reads (when --use-qvs is set)

*.transcripts.hq.bam

hq_pbi (file)

Pacbio index of high quality reads (when --use-qvs is set)

*.transcripts.hq.bam.pbi

lq_bam (file)

Low quality reads (when --use-qvs is set)

*.transcripts.lq.bam

lq_pbi (file)

Pacbio index of low quality reads (when --use-qvs is set)

*.transcripts.lq.bam.pbi

singletons_bam (file)

Unclustered reads (when --singletons is set)

*.transcripts.singletons.bam

singletons_pbi (file)

Pacbio index of unclustered reads (when --singletons is set)

*.transcripts.singletons.bam.pbi

Tools

isoseq3 Documentation

IsoSeq3 - Cluster - Cluster trimmed consensus sequences

License: BSD-3-Clause-Clear
Authors