sRNA Comparison

Author

Steven Roberts

Published

August 16, 2023

https://gannet.fish.washington.edu/Atumefaciens/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed/sRNA-ACR-140-S1-TP2.flexbar_trim.20230621_1.fastq.gz

wget -r \
--no-directories --no-parent \
-P ../data \
-A "_1.fastq.gz" https://gannet.fish.washington.edu/Atumefaciens/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/A_pulchra/trimmed/

gunzip ../data/*gz

cat ../data/sRNA-ACR*fastq | awk 'NR%4==2' | wc -l

cat ../data/sRNA-ACR*fastq | awk 'NR%4==2' | sort | uniq | wc -l

13018677 / 93798121

evermani

https://gannet.fish.washington.edu/Atumefaciens/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed/sRNA-POR-73-S1-TP2.flexbar_trim.20230621_1.fastq.gz

wget -r \
--no-directories --no-parent \
-P ../data \
-A "_1.fastq.gz" https://gannet.fish.washington.edu/Atumefaciens/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_evermanni/trimmed/

gunzip ../data/sRNA-POR*gz

cat ../data/sRNA-POR*fastq | awk 'NR%4==2' | wc -l

cat ../data/sRNA-POR*fastq | awk 'NR%4==2' | sort | uniq | wc -l

Meandrina

https://gannet.fish.washington.edu/Atumefaciens/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/trimmed/sRNA-POC-48-S1-TP2.flexbar_trim.20230621_1.fastq.gz

wget -r \
--no-directories --no-parent \
-P ../data \
-A "_1.fastq.gz" https://gannet.fish.washington.edu/Atumefaciens/20230620-E5_coral-fastqc-flexbar-multiqc-sRNAseq/P_meandrina/trimmed/

gunzip ../data/sRNA-POC*gz

cat ../data/sRNA-POC*fastq | awk 'NR%4==2' | wc -l

cat ../data/sRNA-POC*fastq | awk 'NR%4==2' | sort | uniq | wc -l

blast comparison

cat /home/shared/8TB_HDD_01/sam/data/A_pulchra/sRNAseq/collapsed/*fasta > ../output/apul_coll.fasta

cat /home/shared/8TB_HDD_01/sam/data/P_evermanni/sRNAseq/collapsed/*fasta > ../output/peve_coll.fasta

cat /home/shared/8TB_HDD_01/sam/data/P_meandrina/sRNAseq/collapsed/*fasta > ../output/pmea_coll.fasta

/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ../output/apul_coll.fasta \
-dbtype nucl \
-out ../data/blast/apul_sRNA

/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ../output/peve_coll.fasta \
-dbtype nucl \
-out ../data/blast/peve_sRNA

/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ../output/pmea_coll.fasta \
-dbtype nucl \
-out ../data/blast/pmea_sRNA

ls ../output/*coll*

ls ../data/blast/*sRNA

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../data/apul_bedtools_lncRNAs.fasta \
-db ../data/blast/peve_bedtools_lncRNAs \
-out ../output/apul_peve_blastn.tab \
-evalue 1E-40 \
-num_threads 40 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

wc -l ../output/apul_peve_blastn.tab

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../data/apul_bedtools_lncRNAs.fasta \
-db ../data/blast/pmea_bedtools_lncRNAs \
-out ../output/apul_pmea_blastn.tab \
-evalue 1E-40 \
-num_threads 40 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

wc -l ../output/apul_pmea_blastn.tab

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../data/peve_bedtools_lncRNAs.fasta \
-db ../data/blast/pmea_bedtools_lncRNAs \
-out ../output/peve_pmea_blastn.tab \
-evalue 1E-40 \
-num_threads 40 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

wc -l ../output/peve_pmea_blastn.tab

wc -l ../output/*tab

  1117 ../output/apul_peve_blastn.tab
  1008 ../output/apul_pmea_blastn.tab
   483 ../output/peve_pmea_blastn.tab
  2608 total