This module prepares an isoform classification table and a gene info table

Inputs:

• sqanti classification file
• (removed for this Container for now - kalliso tpm file)
• (removed for this Container for now - kalliso ribodepletion tpm file)
• ensg_to_gene mapping file
• enst_to_isoname mapping file
• gene_len_stats table

Outputs:

• sqanti isoform table
• gene level info table

For running the transcriptome summary per cluster

THE MOST IMPORTANT THING HERE IS THE PRODUCTION OF THE PACBIO-GENE REFERENCE TABLE
In our case here we will have one pacbio-gene reference per cluster

input:
file(sqanti_classification) from ch_sample_classification_transcriptome
file(tpm) from ch_sample_kallisto
file(ribo) from ch_normalized_ribo_kallisto
file(ensg_to_gene) from ch_ensg_gene
file(enst_to_isoname) from ch_enst_isoname
file(len_stats) from ch_gene_lens_transcriptome
output:
file("gene_level_tab.tsv") into ch_gene_level
file("sqanti_isoform_info.tsv") into ch_sqanti_isoform_info
file("pb_gene.tsv") into ch_pb_gene

PacBio IsoSeq files - in this case, these were pulled into Bar-Code Clusters determined by the partner samples short read RNAseq files.

• Each cluster then was annotated with Sqanti
• Each cluster Filtered
• Each cluster Collapsed
• Each cluster Classified

See the singleCellLongReadAnalysis/bin directory for the steps broken down as separate shell scripts.

This transcriptome-summary-docker image is run after having building with GitHub actions the Dockerfile in this repository and publishing it on GitHub.

First step I pulled it locally

docker pull ghcr.io/adeslatt/transcriptome_summary:latest

Docker image build with name transcriptome_summary.

And then I ran the command to run this locally -- this is one example of the long filenames that result as you step through the Long-Read-Proteogenomics Nextflow Workflow main.nf

PWD=$(pwd)

docker run --rm -v $PWD:$PWD -w $PWD -it sixframe six_frame_translation.py \
--iso_annot filtered_Blin_neg_filt_ranked_BC_clust9_B_ccsids.merge5.collapsed_corrected.5degfilter_classification.5degfilter.tsv \
--ensg_gene ensg_gene.tsv \
--sample_fasta filtered_Blin_neg_filt_ranked_BC_clust9_B_ccsids.merge5.collapsed_corrected.5degfilter.fasta \
--output_fasta filtered_Blin_neg_filt_ranked_BC_clust9_B_ccsids.merge5.collapsed_corrected.5degfilter.6frame.fasta