Hey Rob,
This is a conceptual question. I can see in the vamb_minimap_group.slurm that the grouped contigs (contigs.fna.gz) are identified, and each is converted to a .mmi file, if not already present. The code then maps the R1 and R2 reads. It appears to map all R1 and R2 reads (despite the grouping variable: in the current run of this, I have G1 = 45 and G2 = 32). The samples are called from the R1_reads.txt file, which is generated when the string to batch scripts is launched. Should the samples used to create the contig files and thus the mmi files be those (G1=45 and G2=32 samples) that are mapped back to the contig files?
If you map the other samples, will this skew the abundance profiles for the contigs, and therefore alter how contigs are binned?
Thanks for putting all of the code together
mike
Hey Rob,
This is a conceptual question. I can see in the vamb_minimap_group.slurm that the grouped contigs (contigs.fna.gz) are identified, and each is converted to a .mmi file, if not already present. The code then maps the R1 and R2 reads. It appears to map all R1 and R2 reads (despite the grouping variable: in the current run of this, I have G1 = 45 and G2 = 32). The samples are called from the R1_reads.txt file, which is generated when the string to batch scripts is launched. Should the samples used to create the contig files and thus the mmi files be those (G1=45 and G2=32 samples) that are mapped back to the contig files?
If you map the other samples, will this skew the abundance profiles for the contigs, and therefore alter how contigs are binned?
Thanks for putting all of the code together
mike