ONT_pilot_w_GDB_samples.md

@@ -523,7 +523,27 @@ ln -s ../non_methylation_aware_results/assembly/metaspades/ONT3_MG_xx_Rashi_S11/
 rm bwa* mmi*      # removing non-essential files
 
 metaquast.py --max-ref-number 0 --threads 24 *fa -o non_mod_2019_quast_results
-# downloaded both the folders to desktop at ~/Documents/Nanopore_ONT/.
+
+## comparing methylation vs non-methylation assemblies ##
+# running quast to compare methylation vs non-methylation assemblies
+conda activate quast
+cd /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/
+mkdir quast_methylation_v_non_comparison
+cd quast_methylation_v_non_comparison
+
+# getting the methylation assemblies
+ln -s  ../results/assembly/*.fa .
+ln -s ../results/assembly/metaspades/ONT3_MG_xx_Rashi_S11/final.contigs.fna metaspades.fa
+# rename files
+for file in *.fa; do mv "$file" meth_"$file"; done
+
+# getting the non-methylation assemblies
+ln -s ../non_methylation_aware_results/assembly/*.fa .
+ln -s ../non_methylation_aware_results/assembly/metaspades/ONT3_MG_xx_Rashi_S11/final.contigs.fna metaspades.fa
+rm bwa* mmi*      # removing non-essential files
+
+metaquast.py --max-ref-number 0 --threads 24 *fa -o quast_comparision_meth_v_non_results
+# downloaded all the folders to desktop at ~/Documents/Nanopore_ONT/.
 ```
 
 ##### SOURMASH #####