Description

The goal of this project is to identify problems with previous kinnex pipeline that resulted in loss of X and Y sequences, and remap/classify/filter. Mapped bams will be used for downstream RNAseq analysis, isoform identification, etc.

Samples are from R. hastatulus male and female flower buds.

directories and important files

resources/flnc-x.bam - 4 unmapped bam files provided by sickkids sequencing. Original versions in /ohta1/emily.glasgow/Mykhailo_data/Kinnex/WU2U3LR/GLA27952.20240705/GLA27952-Pool_150PM_CELL1/outputs/

main pipeline

workflow/Snakefile - pbmm2 align, isoseq collapse, pigeon prepare, pigeon classify, pigeon filter -
workflow/config.yaml

scripts

To remove small scaffolds (keeping them resulted in the X and Y being lost from the output) and properly format the gtf for Pigeon workflow/scripts/fix_gtf.sh workflow/scripts/fix_ref.sh

gffs and fastas

Original gff/fastas, contains X without the PAR, Y with PAR + all autosomes from the haplotype 2 assembly /ohta2/bianca.sacchi/annotation_TX/noMatPAR_txanno/merged_TX_noMatPAR.fa /ohta2/bianca.sacchi/annotation_TX/noMatPAR_txanno/merged_TX_noMatPARlarge_txanno.gff

Used in pipeline: resources/merged_TX_noMatPAR.modified.gtf resources/merged_TX_noMatPARlarge.fa

original outputs, missing X and Y

/ohta1/emily.glasgow/Mykhailo_data/Kinnex/WU2U3LR/GLA27952.20240705/GLA27952-Pool_150PM_CELL1/outputs symlinked as outputs/ in this directory.

output from my attemps in October 2024

results/ - includes gffs containing classified/clustered isoforms for each sample (separately), flnc counts, etc.