I ran abyss twice on the same genome, one without any extra dataset for scaffolding and the second using linked reads. Both had exactly the same stats values. Is this normal? Shouldn't I expect some minimal differences? I just want to make sure abyss DID use the linked reads for guiding scaffolding.
This is the script I used:
abyss-pe k=27 name=Tdiscoideus2 lr='tet' tet='/home/ngutierrez/nas4/linked_reads_output/barcoded.fastq.gz' in='/home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R1_001.trimmed.fastq.gz /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R2_001.trimmed.fastq.gz'
Barcodes of linked reads were treated using the longranger basic command as indicated in the abyss manual.
Any help would be appreciated,