Entering edit mode
3.2 years ago
karenclarom9
•
0
Hi everyone! I chose SSPACE to form scaffolds and it seemed to work well. I obtained 20 mismatches (N's). But, when I tried to fill gaps with GapFiller, I obtained more mismatches than before: 49. I can´t find out why this is happening, I hope someone could help me, please! I used the same library file for both programs:
lib1 bwa Brady1_1_val_1.fq Brady1_2_val_2.fq 350 0.75 FR
And these are my commands for SSPACE and GapFille (I used the default values each program recommend)
SSPACE_Standard_v3.0.pl -l SSPACE_Brady.config -s contigs.fasta -k 5 -a 0.7 -x 1 -m 32 -o 20 -b SSPACE_brady
GapFiller.pl -l SSPACE_Brady.config -s SPACCE_brady.final.scaffolds.fasta -m 29 -o 2 -d 50 -n 10 -t 10 -r 0.7 -i 10 -b gapfiller_brady
