pipelines-docs

Read Clustering

In this step, the pipeline generates high-quality consensus transcript sequences from Full Length Non Chimeric (FLNC) reads. It accepts and processes one or multiple FLNC BAM files in a single run, producing a unified output. The consensus transcripts are used in downstream alignment, collapsing, and quantification.

Clustering FLNC Reads

Generate high-quality consensus transcripts

isoseq cluster2 --singletons flnc.fofn transcripts.bam

Arguments:

• flnc.fofn: a file-of-filenames (FOFN) listing the FLNC BAM files to be processed together.
• --singletons: includes low-abundance transcripts supported by fewer than two FLNC reads, which are typically excluded. This allows retention of rare transcript isoforms that might still be biologically relevant.

Implementation with IsoSeq

The pipeline uses IsoSeq version 4.2.0.

Source Code

All the relevant code can be accessed in the GitHub repository:

• isoseq_cluster2.sh [cluster2]

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