Variable regions in the same part of the sequence

[sidwekhande]

We would like to define variable polyA and cDNA region lengths in the same part of the sequence. For example, a sequence space of 40bp is a mix of variable polyA and cDNA lengths (both 0-40bp).

A test seqspec that defines this use case is uploaded to syn64109806, along with the corresponding fastqs.

The index command using seqspec v0.3.0 currently returns

seqspec index -m rna -r SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R1.fastq.gz,SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz SHAREseqv2-SS_PKR_500-RNA_updated.yaml

SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R1.fastq.gz	cdna	cdna	0	50
SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz	umi	umi	0	10
SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz	cdna_variable	cdna	10	50
SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz	poly_A	poly_A	50	90
SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz	linker1	linker	90	105
SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz	rna Cell Barcode 1	barcode	105	113
SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz	linker2	linker	113	143
SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz	rna Cell Barcode 2	barcode	143	149

This concatenates the cdna_variable and polyA regions in order and assigns 40bp length to each, and "pushes" the rna Cell Barcode 3 out of the index command, as the defined total length of the sequence (also observed when passing -t kb)

Passing -t kb

seqspec index -m rna -r SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R1.fastq.gz,SS-CoPA-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz -t kb SHAREseqv2-SS_PKR_500-RNA_updated.yaml

1,105,113,1,143,149:1,0,10:0,0,50,1,10,50

Please let me know your thoughts - thanks!