11_MAG_MAPPING

Mapping MAGS back to the read data

1. Import to anvio

# WITHIN THE 11_MAP_MAGS folder on kjempefuru
# concatenate all the contigs from all the "winning" MAGS from dRep:
cat dereplicated_genomes/*fa > NON-REDUNDANT-MAGS.fa

# Runar did not have good deflines tisk tisk, which Anvio complains about. Argh!
# replacing dash, and parentheses with underscore.
sed -i 's/-/_/g; s/(/_/g; s/)/_/g' NON_REDUNDANT_MAGS.fa 


# Then we import the file to anvio to make it a contig.db
anvi-gen-contigs-database -f NON-REDUNDANT-MAGS.fa -o NON-REDUNDANT-MAGs-CONTIGS.db

2. Map reads back

PATH_2019="/export/dahlefs/work/Shotgun/Metagenomes_chimneys_2019/01_QC/"
PATH_2020="/export/dahlefs/work/Metagenomes_chimneys_2020_workfolder/02_HUMAN_Decontam/"
PATH_Runar="/export/dahlefs/work/Runar_AMOR_metagenomes/"

for i in `cat AMOR_only`; do bowtie2 --threads 20 -x NON_REDUNDANT_MAGS \
-1 ${PATH_2020}${i}-cleanR1.fq -2 ${PATH_2020}${i}-cleanR2.fq --no-unal \
-S Bowtie/${i}-in-NRMAGS.sam; 
done

for i in `cat Iron_mats_Good`; do bowtie2 --threads 20 -x NON_REDUNDANT_MAGS \
-1 ${PATH_2020}${i}-cleanR1.fq -2 ${PATH_2020}${i}-cleanR2.fq --no-unal \
-S Bowtie/${i}-in-NRMAGS.sam; 
done

for i in `cat AMOR_2019`; do bowtie2 --threads 20 -x NON_REDUNDANT_MAGS \
-1 ${PATH_2019}${i}-QUALITY_PASSED_R1.fastq -2 ${PATH_2019}${i}-QUALITY_PASSED_R2.fastq \
--no-unal -S Bowtie/${i}-in-NRMAGS.sam; 
done


for i in `cat sample_list_noNP`; do bowtie2 --threads 20 -x NON_REDUNDANT_MAGS \
-1 ${PATH_Runar}${i}_S1_L001_R1_001.fastq -2 ${PATH_Runar}${i}_S1_L001_R2_001.fastq --no-unal \
-S Bowtie/${i}-in-NRMAGS.sam; done

3. Covert .sam to .bam. Index with samtools and remove temp files.

4. Emily and Achim put MAG names in Runar's bin FASTA contig headers. for sample in *.fa;
   do pref=$(basename "$sample" .fa); inew=${pref//./}; inew2=${inew//-/};
   anvi-script-reformat-fasta ${sample} --simplify-names --prefix _${inew2}
   -o Renamed_MAGs_Runar/${sample};
   done