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nf-core/gstama/collapse @ 0.0.0-6c4ed3a

Collapse redundant transcript models in Iso-Seq data.

tama_collapse.py isoseq nanopore long-read transcriptome gene model TAMA
Latest version: 0.0.0-6c4ed3a
Total downloads: 8
Source: nf-core/modules
Authors: @sguizard
Maintainers: @sguizard

Summary

Collapse redundant transcript models in Iso-Seq data.

Get started

Add the following snippet to your workflow script to include this module.

include { GSTAMA_COLLAPSE } from 'nf-core/gstama/collapse'

License

MIT License

Process
Name GSTAMA_COLLAPSE
Input 2 channels
#1 tuple
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 10 channels
#1 bed tuple
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
#2 read tuple
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
#3 polya tuple
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
#4 varcov tuple
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
#5 variants tuple
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
#6 versions
versions.yml file

File containing software versions

 versions.yml
#7 strand_check tuple
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
#8 trans_report tuple
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
#9 bed_trans_reads tuple
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
#10 local_density_error tuple
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
Tool Description Homepage
tama_collapse.py Collapse similar gene model