A pulcra kallisto

/home/shared/kallisto/kallisto -h

/home/shared/kallisto/kallisto \
index -i \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.index \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna

ls ../data/S*

1 Amil2.1

 /home/shared/kallisto/kallisto \
quant -i ../data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.index \
-o ../output/03-kallisto/mil_SRR8601366 \
-t 40 \
../data/SRR8601366_1.fastq ../data/SRR8601366_2.fastq \
2>&1 | tee ../output/03-kallisto/mil_SRR8601366.out

 /home/shared/kallisto/kallisto \
quant -i ../data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.index \
-o ../output/03-kallisto/mil02_SRR8601366 \
-t 40 \
--genomebam \
--gtf ../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gff \
../data/SRR8601366_1.fastq ../data/SRR8601366_2.fastq \
2>&1 | tee ../output/03-kallisto/mil02_SRR8601366.out

 /home/shared/kallisto/kallisto \
quant -i ../data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.index \
-o ../output/03-kallisto/mil03_SRR8601366 \
-t 40 \
--genomebam \
--gtf ../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf \
../data/SRR8601366_1.fastq ../data/SRR8601366_2.fastq \
2>&1 | tee ../output/03-kallisto/mil03_SRR8601366.out

2 Adig

/home/shared/kallisto/kallisto \
index -i \
../data/Adig/ncbi_dataset/data/GCF_000222465.1/GCF_000222465.1_Adig_1.1_genomic.index \
../data/Adig/ncbi_dataset/data/GCF_000222465.1/GCF_000222465.1_Adig_1.1_genomic.fna

 /home/shared/kallisto/kallisto \
quant -i ../data/Adig/ncbi_dataset/data/GCF_000222465.1/GCF_000222465.1_Adig_1.1_genomic.index \
-o ../output/03-kallisto/dig_SRR8601366 \
-t 40 \
../data/SRR8601366_1.fastq ../data/SRR8601366_2.fastq \
2>&1 | tee ../output/03-kallisto/dig_SRR8601366.out

3 Ahya

/home/shared/kallisto/kallisto \
index -i \
../data/Ahya/ncbi_dataset/data/GCA_020536085.1/GCA_020536085.1_Ahyacinthus.chrsV1_genomic.index \
../data/Ahya/ncbi_dataset/data/GCA_020536085.1/GCA_020536085.1_Ahyacinthus.chrsV1_genomic.fna

 /home/shared/kallisto/kallisto \
quant -i ../data/Ahya/ncbi_dataset/data/GCA_020536085.1/GCA_020536085.1_Ahyacinthus.chrsV1_genomic.index \
-o ../output/03-kallisto/hya_SRR8601366 \
-t 40 \
../data/SRR8601366_1.fastq ../data/SRR8601366_2.fastq \
2>&1 | tee ../output/03-kallisto/hya_SRR8601366.out

4 Comparing alignment rates

grep 'p_' ../output/03-kallisto/dig_SRR8601366/run_info.json

##  "p_pseudoaligned": 72.8,
##  "p_unique": 69.8,

grep 'p_' ../output/03-kallisto/mil_SRR8601366/run_info.json

##  "p_pseudoaligned": 84.9,
##  "p_unique": 82.2,

grep 'p_' ../output/03-kallisto/mil02_SRR8601366/run_info.json

##  "p_pseudoaligned": 84.9,
##  "p_unique": 82.2,

grep 'p_' ../output/03-kallisto/mil03_SRR8601366/run_info.json

##  "p_pseudoaligned": 84.9,
##  "p_unique": 82.2,

grep 'p_' ../output/03-kallisto/hya_SRR8601366/run_info.json

##  "p_pseudoaligned": 82.1,
##  "p_unique": 80.4,

echo "A hyacinthus"
grep 'p_' ../output/03-kallisto/hya_SRR8601366/run_info.json
echo "A millipora"
grep 'p_' ../output/03-kallisto/mil_SRR8601366/run_info.json
echo "A digitera"
grep 'p_' ../output/03-kallisto/dig_SRR8601366/run_info.json

## A hyacinthus
##  "p_pseudoaligned": 82.1,
##  "p_unique": 80.4,
## A millipora
##  "p_pseudoaligned": 84.9,
##  "p_unique": 82.2,
## A digitera
##  "p_pseudoaligned": 72.8,
##  "p_unique": 69.8,