Low coverage phenotype association with angsd - barrettlab/2021-Genomics-bootcamp GitHub Wiki

1. Copy the fastq.gz files to working directory

sudo cp /data/ccorbett/reads/Barrett-Cameron_AL-MAD-1-1_S51_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_AL-TUS-1-1_S53_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_AR-Was-2-2_S90_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_GA-BAR-2-1_S55_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_IL-JOHN-1-3_S14_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_NC-SP-2-1_S57_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_TN-KNO-3C-2-1_S22_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_TN-LPG-1-1_S59_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_NY-TOM-6M-1-1_S20_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_NJ-CUMB_1-1_S5_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_MD-HOW_1-2_S10_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_PA-BUT-1-1_S16_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_PA-MONT_1-1_S3_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_WI-LAC_2-1_S8_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_WV-PRD_2-4_198_S84_L001* . ;
sudo cp /data/ccorbett/reads/Barrett-Cameron_NY-TOM-IC-1-1_S18_L001* . ;

2. Create a phenotype file (awns absent/present, list awned first)

nano pheno.txt

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3. Unzip the files with pigz -d

pigz -d *.fastq.gz

4. Subsample 10 million reads from each file

for i in *.fastq ;
	do 
		seqtk sample $i 10000000 > sub_${i%}.fastq ;
	done

5. rename the files

rename 's/^sub_Barrett-Cameron/sub_awn/' sub_Barrett-Cameron*
rename 's/.fastq.fastq$/.fastq/' *.fastq.fastq

6. Manually change all awnless accession names from 'awn' to 'awnless'

7. make a samples file for ISSRseq pipeline

ls *R1.fastq | sed 's/_R1.fastq//g' > ../samples.txt

8. Run read trimming with bbmap and index the reference genome

nohup ISSRseq_ReferenceBased.sh -O Test_JS_nuclear -I reads -S samples.txt -R JS_allchr23.fasta -T 30 -M 55 -H 0 -P primers.txt -X 50 &

9. Use bbmap to map reads, create bam files

nohup ISSRseq_CreateBAMs.sh -O Test_JS_nuclear_2022_03_06_09_45 -T 30 &