Description

Collapse redundant transcript models in Iso-Seq data.

Input

name:type
description
pattern

meta:map

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

bam:file

A sorted BAM or sam file of aligned reads

*.{bam,sam}

fasta:file

A fasta file of the genome used for the mapping

*.{fasta,fa}

Output

name:type
description
pattern

bed

meta:map

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

*_collapsed.bed:file

a bed12 format file containing the final collapsed version of your transcriptome

*.bed

bed_trans_reads

meta:map

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

*_trans_read.bed:file

This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5’ degraded read can match to multiple 5’ longer transcript models.

*_trans_read.bed

local_density_error

meta:map

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

*_local_density_error.txt:file

This file contains the log of filtering for local density error around the splice junctions (“-lde”)

*_local_density_error.txt

polya

meta:map

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

*_polya.txt:file

This file contains the reads with potential poly A truncation.

*_polya.txt

read

meta:map

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

*_read.txt:file

This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file

*_read.txt

strand_check

meta:map

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

*_strand_check.txt:file

This file shows instances where the sam flag strand information contrasted the GMAP strand information.

*_strand_check.txt

trans_report

meta:map

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

*_trans_report.txt:file

This file contains collapsing information for each transcript.

*_trans_report.txt

versions

versions.yml:file

File containing software versions

versions.yml

varcov

meta:map

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

*_varcov.txt:file

This file contains the coverage information for each variant detected.

*_varcov.txt

variants

meta:map

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

*_variants.txt:file

This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo.

*_variants.txt