11-kallisto

Reads

ls /home/shared/8TB_HDD_02/graceac9/data/pycno2021/*

/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-19_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-19_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-23_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-23_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-24_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-24_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-34_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-34_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-35_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-35_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-36_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-36_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-37_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-37_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-38_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-38_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-39_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-39_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-40_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-40_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-42_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-42_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-43_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-43_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-48_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-48_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-49_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-49_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-52_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-52_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-54_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-54_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-56_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-56_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-57_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-57_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-58_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-58_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-59_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-59_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-61_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-61_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-63_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-63_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-64_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-64_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-67_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-67_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-69_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-69_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-71_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-71_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-73_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-73_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-75_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-75_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-76_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-76_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-78_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-78_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-81_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-81_R2_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-83_R1_001.fastq.gz.fastp-trim.20220810.fq.gz
/home/shared/8TB_HDD_02/graceac9/data/pycno2021/PSC-83_R2_001.fastq.gz.fastp-trim.20220810.fq.gz

indexing

head /home/shared/8TB_HDD_02/graceac9/GitHub/project-pycno-sizeclass-2022/data/augustus.hints.codingseq

>g3450.t1
ATGAACTACCGGACTGATGATGAAATATATGAAGATGAGGTGGACGAGGAGACAAAACTG
CATCACAGAATTGATGAGCGTGGAGTGAACGGAACTGATTCTCGAGATGAACCAACAAGA
GTTCCTCCAGCCAAGCAGCTGAAGATTCAAGCACCAGTATTGGCGTCTCGGCTCCAGCTG
GAAGCAGTGAGGCGGCCCCACCCCCCTCCTCTTCATCCTCCTCAGATCCACCTGTACCTA
GAACCACACCTAGAGGCATTACAACAGCGTTGTGATAGCTACAAAGGCATTGTTGGATAA
>g3451.t1
ATGAAGATCAACAAAGAAAAATCCAAAGTGATGCATTTGTCTCGCTGCAAAACACCCACG
GACGAGCATCTTCCACATTACACACTGCAAGAGACACAGAGCAAACTGTTCTGCAGACTG
AAGGGGCTGAGAGATTACAACTTTCGCAGTTTCATTCTGGCCTTTCTGCAGTACAATCCA

/home/shared/kallisto/kallisto index \
-i ../analyses/11-kallisto/Ph.codingseq.index \
/home/shared/8TB_HDD_02/graceac9/GitHub/project-pycno-sizeclass-2022/data/augustus.hints.codingseq

find /home/shared/8TB_HDD_02/graceac9/data/pycno2021/*_R1_001.fastq.gz.fastp-trim.20220810.fq.gz \
| xargs -I{} basename -s _R1_001.fastq.gz.fastp-trim.20220810.fq.gz {} \
| xargs -I{} sh -c '/home/shared/kallisto/kallisto quant \
-i ../analyses/11-kallisto/Ph.codingseq.index \
-o ../analyses/11-kallisto/kallisto_01/{} \
-t 10 \
--fr-stranded /home/shared/8TB_HDD_02/graceac9/data/pycno2021/{}_R1_001.fastq.gz.fastp-trim.20220810.fq.gz \
--rf-stranded /home/shared/8TB_HDD_02/graceac9/data/pycno2021/{}_R2_001.fastq.gz.fastp-trim.20220810.fq.gz \
> ../analyses/11-kallisto/{}_kall01.stdout 2> ../analyses/11-kallisto/{}_kall01.stderr'

find /home/shared/8TB_HDD_02/graceac9/data/pycno2021/*_R1_001.fastq.gz.fastp-trim.20220810.fq.gz \
| xargs -I{} basename -s _R1_001.fastq.gz.fastp-trim.20220810.fq.gz {} \
| xargs -I{} sh -c '/home/shared/kallisto/kallisto quant \
-i /home/shared/8TB_HDD_03/sr320/github/fish541-rnaseq/data/Phel_transcriptome.index \
-o ../analyses/11-kallisto/kallisto_02/{} \
-t 36 \
--fr-stranded /home/shared/8TB_HDD_02/graceac9/data/pycno2021/{}_R1_001.fastq.gz.fastp-trim.20220810.fq.gz \
--rf-stranded /home/shared/8TB_HDD_02/graceac9/data/pycno2021/{}_R2_001.fastq.gz.fastp-trim.20220810.fq.gz \
> ../analyses/11-kallisto/{}_kall02.stdout 2> ../analyses/11-kallisto/{}_kall02.stderr'

eval "$(/opt/anaconda/anaconda3/bin/conda shell.bash hook)"
conda activate
which multiqc


multiqc ../analyses/11-kallisto/ \
-o ../analyses/11-kallisto/