IsoSeq - Cluster - Cluster trimmed consensus sequences
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
bam{:bash}
:file
BAM file generated by isoseq refine
*.bam
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.transcripts.bam{:bash}
BAM file of clustered consensus
*.transcripts.bam
pbi{:bash}
*.transcripts.bam.pbi{:bash}
Pacbio Index of consensus reads generated by clustering
*.transcripts.bam.pbi
cluster{:bash}
*.transcripts.cluster{:bash}
A two columns (from, to) file describing original read name to new read name
*.transcripts.cluster
cluster_report{:bash}
*.transcripts.cluster_report.csv{:bash}
A table files clusters (transcripts) members (read)
*.transcripts.cluster_report.csv
transcriptset{:bash}
*.transcripts.transcriptset.xml{:bash}
A metadata xml file which contains full paths to data files
*.transcripts.transcriptset.xml
hq_bam{:bash}
*.transcripts.hq.bam{:bash}
High quality reads (when —use-qvs is set)
*.transcripts.hq.bam
hq_pbi{:bash}
*.transcripts.hq.bam.pbi{:bash}
Pacbio index of high quality reads (when —use-qvs is set)
*.transcripts.hq.bam.pbi
lq_bam{:bash}
*.transcripts.lq.bam{:bash}
Low quality reads (when —use-qvs is set)
*.transcripts.lq.bam
lq_pbi{:bash}
*.transcripts.lq.bam.pbi{:bash}
Pacbio index of low quality reads (when —use-qvs is set)
*.transcripts.lq.bam.pbi
singletons_bam{:bash}
*.transcripts.singletons.bam{:bash}
Unclustered reads (when —singletons is set)
*.transcripts.singletons.bam
singletons_pbi{:bash}
*.transcripts.singletons.bam.pbi{:bash}
Pacbio index of unclustered reads (when —singletons is set)
*.transcripts.singletons.bam.pbi
versions{:bash}
versions.yml{:bash}
File containing software version
versions.yml
