Master

• merging master to checkpoint_snakefile

2019_GDB/scripts/get_mappability.sh

+#!/bin/bash -l
+# Usage: sbatch -t 1:00:00 -N 1 -n 4 get_mappability.sh
+
+date
+cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/results/mapping
+conda activate anvio6       # or any environment that as "samtools"
+
+# metaG
+samtools flagstat sr/bwa_mem/ONT3_MG_xx_Rashi_S11_reads-x-ONT3_MG_xx_Rashi_S11-megahit_contigs.bam > sr_mappability.txt
+samtools flagstat lr/merged/no_barcode/no_barcode_reads-x-no_barcode-flye_contigs.bam > lr_mappability.txt
+
+samtools flagstat bwa_merged_metaspades_hybrid/bwa_merged_metaspades_hybrid.bam > hybrid_bwa_merged.txt 
+samtools flagstat bwa_sr_metaspades_hybrid/bwa_sr_metaspades_hybrid.bam > hybrid_bwa_sr.txt
+samtools flagstat bwa_lr_metaspades_hybrid/bwa_lr_metaspades_hybrid.bam > hybrid_bwa_lr.txt
+
+samtools flagstat mmi_merged_metaspades_hybrid/mmi_merged_metaspades_hybrid.bam > hybrid_mmi_merged.txt
+samtools flagstat mmi_sr_metaspades_hybrid/mmi_sr_metaspades_hybrid.bam > hybrid_mmi_sr.txt
+samtools flagstat mmi_lr_metaspades_hybrid/mmi_lr_metaspades_hybrid.bam > hybrid_mmi_lr.txt
+
+# metaT
+samtools flagstat ./metaT/sr/FastSelectHalf1_MT_Rashi_S12_reads-x-lr_no_barcode_sr_ONT3_MG_xx_Rashi_S11-metaspades_hybrid_contigs.bam > hybrid_metaT_sr.txt
+samtools flagstat ./metaT/sr/FastSelectHalf1_MT_Rashi_S12_reads-x-ONT3_MG_xx_Rashi_S11-megahit_contigs.bam > megahit_metaT_sr.txt
+ 
+# collating all the results in one place
+for file in *.txt; do echo $file; egrep 'total | mapped' $file | head -n 2; done | paste - - - | \
+   sed $'1 i\\\nsample\ttotal\tmapped\tpercent_mapped' | sed 's/ + 0 in total (QC-passed reads + QC-failed reads)//g' | \
+     sed s'/ + 0 mapped//g' | sed 's/ : N\/A)//g' | sed s'/(//g' | sed s'/.txt//g' | \
+       awk '{print$0=$1"\t"$2"\t"$3"\t"$4}' > mappability_index.tsv
+       
+date
\ No newline at end of file