E5 Deepdive Mirna Targetprediction
Options for 3’ UTR prediction
- Gene Ext (see github)
- Calling 1000 bases ahead of gene the UTR and making sure no gene overlap occurs
- Looking at other cnidarian species for 3’ UTR lengths
On my local computer, make fasta file with the given miRNA names.
cd /Users/jillashey/Desktop/PutnamLab/Repositories/deep-dive/DEF-cross-species/output/10-shortRNA-ShortStack-comparison
awk -F, 'NR>1 {print ">" $22 "\n" $11}' Apul_results_mature_named.csv > Apul_results_mature_named.fasta
awk -F, 'NR>1 {print ">" $22 "\n" $11}' Peve_results_mature_named.csv > Peve_results_mature_named.fasta
awk -F, 'NR>1 {print ">" $22 "\n" $11}' Ptuh_results_mature_named.csv > Ptuh_results_mature_named.fasta
Copy the fasta files to the server
cd /data/putnamlab/jillashey/e5
mkdir mirna_seqs
cd mirna_seqs
Apul
Since the Apul genome is assembled and the annotation is finishing up, the rest of e5 data analysis will proceed with the Apul genome instead of the Amil genome. Therefore, I need to identify the 3’UTR ends because that is what miranda requires to run.
Identify the counts of each feature from the gff file
cd /data/putnamlab/jillashey/e5/refs
GFF_FILE="/data/putnamlab/tconn/predict_results/Acropora_pulchra.gff3"
genome="/data/putnamlab/REFS/Apul/apul.hifiasm.s55_pa.p_ctg.fa.k32.w100.z1000.ntLink.5rounds.masked.fa"
grep -v '^#' ${GFF_FILE} | cut -s -f 3 | sort | uniq -c | sort -rn > all_features_apul.txt
209537 exon
201613 CDS
44371 gene
36447 mRNA
7924 tRNA
No UTRs annotated. This is expected, as Trinity is still finishing up the Apul genome annotation. Extract gene as a feature types and generate individual gff for the gene feature. The mRNA feature will be used to as a spatial reference to create 3’UTRs. Gene will not be used because the genes also code for tRNAs.
grep $'\tmRNA\t' ${GFF_FILE} > apul_GFFannotation.mRNA.gff
Extract scaffold lengths
cat is ${genome} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' > apul.Chromosome_lenghts.txt
wc -l apul.Chromosome_lenghts.txt
174 apul.Chromosome_lenghts.txt
Extract scaffold names
awk -F" " '{print $1}' apul.Chromosome_lenghts.txt > apul.Chromosome_names.txt
The following script will sort the mRNA gff, extract 1kb down the 3’ end of mRNA, subtract portions of the 1kb flank (representing the 3’UTR) from any overlapping mRNA, and make fasta file of the 3’UTRs. In the e5 scripts folder: nano bed_apul.sh
#!/bin/bash
#SBATCH -t 24:00:00
#SBATCH --nodes=1 --ntasks-per-node=5
#SBATCH --export=NONE
#SBATCH --mem=250GB
#SBATCH --mail-type=BEGIN,END,FAIL #email you when job starts, stops and/or fails
#SBATCH --mail-user=jillashey@uri.edu #your email to send notifications
#SBATCH --account=putnamlab
#SBATCH -D /data/putnamlab/jillashey/e5/scripts
#SBATCH -o slurm-%j.out
#SBATCH -e slurm-%j.error
module load BEDTools/2.30.0-GCC-11.3.0
cd /data/putnamlab/jillashey/e5/refs
echo "Sorting gffs by chromosome" $(date)
sortBed -faidx apul.Chromosome_names.txt -i apul_GFFannotation.mRNA.gff > apul_GFFannotation.mRNA_sorted.gff
echo "Sorting complete!" $(date)
echo "Extracting 1kb 3' UTRs" $(date)
bedtools flank -i apul_GFFannotation.mRNA_sorted.gff -g apul.Chromosome_lenghts.txt -l 0 -r 1000 -s | awk '{gsub("gene","3prime_UTR",$3); print $0 }' | awk '{if($5-$4 > 3)print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9}' | tr ' ' '\t' > apul.GFFannotation.3UTR_1kb.gff
echo "Subtract portions of UTRs that overlap nearby genes" $(date)
bedtools subtract -a apul.GFFannotation.3UTR_1kb.gff -b apul_GFFannotation.mRNA_sorted.gff > apul.GFFannotation.3UTR_1kb_corrected.gff
echo "3' UTRs identified!" $(date)
echo "Extracting 3' UTR sequences" $(date)
bedtools getfasta -fi /data/putnamlab/REFS/Apul/apul.hifiasm.s55_pa.p_ctg.fa.k32.w100.z1000.ntLink.5rounds.masked.fa -bed apul.GFFannotation.3UTR_1kb_corrected.gff -fo apul_3UTR_1kb.fasta -fullHeader
echo "Sequence extraction complete!" $(date)
Submitted batch job 341153. Ran very fast.
zgrep -c ">" apul_3UTR_1kb.fasta
37359
Time to run miranda for Apul. In the e5 scripts folder: nano miranda_strict_all_1kb_apul.sh
#!/bin/bash -i
#SBATCH -t 48:00:00
#SBATCH --nodes=1 --ntasks-per-node=10
#SBATCH --export=NONE
#SBATCH --mem=500GB
#SBATCH --mail-type=BEGIN,END,FAIL #email you when job starts, stops and/or fails
#SBATCH --mail-user=jillashey@uri.edu #your email to send notifications
#SBATCH --account=putnamlab
#SBATCH -D /data/putnamlab/jillashey/e5/scripts
#SBATCH -o slurm-%j.out
#SBATCH -e slurm-%j.error
echo "Apul starting miranda run with all genes and miRNAs with score cutoff >100, energy cutoff <-10, and strict binding invoked"$(date)
module load Miniconda3/4.9.2
conda activate /data/putnamlab/conda/miranda
miranda /data/putnamlab/jillashey/e5/mirna_seqs/Apul_results_mature_named.fasta /data/putnamlab/jillashey/e5/refs/apul_3UTR_1kb.fasta -sc 100 -en -10 -strict -out /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_apul.tab
conda deactivate
echo "miranda run finished!"$(date)
echo "counting number of putative interactions predicted" $(date)
zgrep -c "Performing Scan" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_apul.tab
echo "Parsing output" $(date)
grep -A 1 "Scores for this hit:" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_apul.tab | sort | grep '>' > /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_apul.txt
echo "counting number of putative interactions predicted" $(date)
wc -l /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_apul.txt
echo "Apul miranda script complete" $(date)
Submitted batch job 341156. Started running immediately.
using the Amil genome ?
Identify counts of each feature from gff
cd /data/putnamlab/jillashey/genome/Amil_v2.01
grep -v '^#' GCF_013753865.1_Amil_v2.1_genomic.gff | cut -s -f 3 | sort | uniq -c | sort -rn > all_features_apul_amil.txt
390533 exon
317969 CDS
41860 mRNA
36904 gene
22387 cDNA_match
6128 lnc_RNA
5871 pseudogene
2066 transcript
1413 tRNA
854 region
283 rRNA
170 snRNA
62 snoRNA
1 guide_RNA
Generate gff for genes
grep $'\tgene\t' GCF_013753865.1_Amil_v2.1_genomic.gff > Amil_gene.gtf
Extract scaffold lengths.
sed 's/^\(>[^ ]*\).*/\1/' GCF_013753865.1_Amil_v2.1_genomic.fna > GCF_013753865.1_Amil_v2.1_genomic_modified.fna
cat is GCF_013753865.1_Amil_v2.1_genomic_modified.fna | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' > Amil_Chromosome_lengths.txt
Extract scaffold names
awk -F" " '{print $1}' Amil_Chromosome_lengths.txt > Amil_Chromosome_names.txt
Create 1kb 3’UTR in gff
interactive
module load BEDTools/2.30.0-GCC-11.3.0
bedtools flank -i Amil_gene.gtf -g Amil_Chromosome_lengths.txt -l 0 -r 1000 -s | awk '{gsub("gene","3prime_UTR",$3); print $0 }' | awk '{if($5-$4 > 3)print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9}' | tr ' ' '\t' > Amil_3UTR_1kb.gtf
Subtract portions of 3’UTR that overlap nearby genes
bedtools subtract -a Amil_3UTR_1kb.gtf -b Amil_gene.gtf > Amil_3UTR_1kb_corrected.gtf
Extract 3’UTR sequences from genome
awk '{print $1 "\t" $4-1 "\t" $5 "\t" $9 "\t" "." "\t" $7}' Amil_3UTR_1kb_corrected.gtf | sed 's/"//g' > Amil_3UTR_1kb_corrected.bed
bedtools getfasta -fi GCF_013753865.1_Amil_v2.1_genomic_modified.fna -bed Amil_3UTR_1kb_corrected.bed -fo Amil_3UTR_1kb.fasta -name
Run miranda for Apul data using Amil genome. In the scripts folder: nano miranda_strict_all_1kb_amil_apul.sh
#!/bin/bash -i
#SBATCH -t 48:00:00
#SBATCH --nodes=1 --ntasks-per-node=10
#SBATCH --export=NONE
#SBATCH --mem=500GB
#SBATCH --mail-type=BEGIN,END,FAIL #email you when job starts, stops and/or fails
#SBATCH --mail-user=jillashey@uri.edu #your email to send notifications
#SBATCH --account=putnamlab
#SBATCH -D /data/putnamlab/jillashey/e5/scripts
#SBATCH -o slurm-%j.out
#SBATCH -e slurm-%j.error
echo "Apul using Amil genome starting miranda run with all genes and miRNAs with energy cutoff <-20 and strict binding invoked"$(date)
module load Miniconda3/4.9.2
conda activate /data/putnamlab/conda/miranda
miranda /data/putnamlab/jillashey/e5/mirna_seqs/Apul_results_mature_named.fasta /data/putnamlab/jillashey/genome/Amil_v2.01/Amil_3UTR_1kb.fasta -en -20 -strict -out /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_amil_apul.tab
conda deactivate
echo "miranda run finished!"$(date)
echo "counting number of putative interactions predicted" $(date)
zgrep -c "Performing Scan" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_amil_apul.tab
echo "Parsing output" $(date)
grep -A 1 "Scores for this hit:" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_amil_apul.tab | sort | grep '>' > /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_amil_apul.txt
echo "counting number of putative interactions predicted" $(date)
wc -l /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_amil_apul.txt
echo "Apul using Amil genome miranda script complete" $(date)
Submitted batch job 346077. Results:
counting number of putative interactions predicted Wed Oct 30 16:54:24 EDT 2024
1227134
Parsing output Wed Oct 30 16:54:29 EDT 2024
counting number of putative interactions predicted Wed Oct 30 16:54:30 EDT 2024
4144 /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_amil_apul.txt
Peve
To run miranda, I need to identify the 3’ UTR ends.
First, identify counts of each feature from gff file
GFF_FILE="/data/putnamlab/jillashey/genome/Peve/Porites_evermanni_v1.annot.gff"
genome="/data/putnamlab/jillashey/genome/Peve/Porites_evermanni_v1.fa"
grep -v '^#' ${GFF_FILE} | cut -s -f 3 | sort | uniq -c | sort -rn > all_features_peve.txt
231320 CDS
40389 mRNA
15098 UTR
There are a decent amount of UTRs annotated in the Peve gff but they aren’t differentiated between 5’ and 3’. Calculate the length of the 3’ UTRs.
awk '$3 == "UTR" {print $0, $5 - $4 + 1}' OFS="\t" Porites_evermanni_v1.annot.gff > UTR_lengths_Peve.txt
awk '{sum += $NF} END {if (NR > 0) print sum / NR}' UTR_lengths_Peve.txt
Average length of UTRs is 296.414. Extract feature types and generate individual gffs for each feature.
grep $'\tCDS\t' ${GFF_FILE} > peve_GFFannotation.CDS.gff
grep $'\tmRNA\t' ${GFF_FILE} > peve_GFFannotation.mRNA.gff
grep $'\tUTR\t' ${GFF_FILE} > peve_GFFannotation.UTR.gff
Extract scaffold lengths
cat is ${genome} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' > peve.Chromosome_lenghts.txt
wc -l peve.Chromosome_lenghts.txt
8186 peve.Chromosome_lenghts.txt
Extract scaffold names
awk -F" " '{print $1}' peve.Chromosome_lenghts.txt > peve.Chromosome_names.txt
I’m going to combine all of the bed stuff into one script. In the e5 scripts folder: nano bed_peve.sh
#!/bin/bash
#SBATCH -t 24:00:00
#SBATCH --nodes=1 --ntasks-per-node=5
#SBATCH --export=NONE
#SBATCH --mem=250GB
#SBATCH --mail-type=BEGIN,END,FAIL #email you when job starts, stops and/or fails
#SBATCH --mail-user=jillashey@uri.edu #your email to send notifications
#SBATCH --account=putnamlab
#SBATCH -D /data/putnamlab/jillashey/e5/scripts
#SBATCH -o slurm-%j.out
#SBATCH -e slurm-%j.error
module load BEDTools/2.30.0-GCC-11.3.0
cd /data/putnamlab/jillashey/genome/Peve
echo "Sorting gffs by chromosome" $(date)
sortBed -faidx peve.Chromosome_names.txt -i peve_GFFannotation.CDS.gff > peve_GFFannotation.CDS_sorted.gff
sortBed -faidx peve.Chromosome_names.txt -i peve_GFFannotation.mRNA.gff > peve_GFFannotation.mRNA_sorted.gff
sortBed -faidx peve.Chromosome_names.txt -i peve_GFFannotation.UTR.gff > peve_GFFannotation.UTR_sorted.gff
echo "Sorting complete!" $(date)
echo "Extracting 1kb 3' UTRs" $(date)
bedtools flank -i peve_GFFannotation.mRNA_sorted.gff -g peve.Chromosome_lenghts.txt -l 0 -r 1000 -s | awk '{gsub("gene","3prime_UTR",$3); print $0 }' | awk '{if($5-$4 > 3)print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9}' | tr ' ' '\t' > peve.GFFannotation.3UTR_1kb.gff
echo "Subtract portions of UTRs that overlap nearby genes" $(date)
bedtools subtract -a peve.GFFannotation.3UTR_1kb.gff -b peve_GFFannotation.mRNA_sorted.gff > peve.GFFannotation.3UTR_1kb_corrected.gff
echo "3' UTRs identified!" $(date)
echo "Extracting 3' UTR sequences" $(date)
bedtools getfasta -fi Porites_evermanni_v1.fa -bed peve.GFFannotation.3UTR_1kb_corrected.gff -fo peve_3UTR_1kb.fasta -fullHeader
echo "Sequence extraction complete!" $(date)
Submitted batch job 340834. Done! Now run miranda for the Peve data. In the scripts folder: nano miranda_strict_all_1kb_peve.sh
#!/bin/bash -i
#SBATCH -t 200:00:00
#SBATCH --nodes=1 --ntasks-per-node=10
#SBATCH --export=NONE
#SBATCH --mem=500GB
#SBATCH --mail-type=BEGIN,END,FAIL #email you when job starts, stops and/or fails
#SBATCH --mail-user=jillashey@uri.edu #your email to send notifications
#SBATCH --account=putnamlab
#SBATCH -D /data/putnamlab/jillashey/e5/scripts
#SBATCH -o slurm-%j.out
#SBATCH -e slurm-%j.error
echo "PEVE starting miranda run with all genes and miRNAs with score cutoff >100, energy cutoff <-10, and strict binding invoked"$(date)
module load Miniconda3/4.9.2
conda activate /data/putnamlab/conda/miranda
miranda /data/putnamlab/jillashey/e5/mirna_seqs/Peve_results_mature_named.fasta /data/putnamlab/jillashey/genome/Peve/peve_3UTR_1kb.fasta -sc 100 -en -10 -strict -out /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_peve.tab
conda deactivate
echo "miranda run finished!"$(date)
echo "counting number of putative interactions predicted" $(date)
zgrep -c "Performing Scan" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_peve.tab
echo "Parsing output" $(date)
grep -A 1 "Scores for this hit:" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_peve.tab | sort | grep '>' > /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_peve.txt
echo "counting number of putative interactions predicted" $(date)
wc -l /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_peve.txt
echo "PEVE miranda script complete" $(date)
Submitted batch job 340835. Ran in about 1.5 hours.
head miranda_strict_all_1kb_parsed_peve.txt
>peve-mir-100 Porites_evermani_scaffold_1005:62085-63085 144.00 -16.87 2 17 1 16 15 66.67% 73.33%
>peve-mir-100 Porites_evermani_scaffold_100:97079-98079 140.00 -16.46 2 9 376 395 7 100.00% 100.00%
>peve-mir-100 Porites_evermani_scaffold_101:185725-186725 142.00 -14.24 2 11 850 869 9 88.89% 88.89%
>peve-mir-100 Porites_evermani_scaffold_1027:48934-49934 140.00 -17.00 2 9 543 562 7 100.00% 100.00%
>peve-mir-100 Porites_evermani_scaffold_104:288813-289813 146.00 -19.73 2 19 931 947 17 70.59% 76.47%
>peve-mir-100 Porites_evermani_scaffold_1047:141562-142562 142.00 -16.36 2 11 148 167 9 88.89% 88.89%
>peve-mir-100 Porites_evermani_scaffold_1050:86266-86716 145.00 -16.55 2 10 333 352 8 100.00% 100.00%
>peve-mir-100 Porites_evermani_scaffold_106:362578-363578 144.00 -17.12 2 15 221 239 13 76.92% 84.62%
>peve-mir-100 Porites_evermani_scaffold_1066:63731-64731 150.00 -17.45 2 18 600 617 16 75.00% 81.25%
>peve-mir-100 Porites_evermani_scaffold_1082:85736-86736 155.00 -21.77 2 16 964 983 14 78.57% 85.71%
wc -l miranda_strict_all_1kb_parsed_peve.txt
97782 miranda_strict_all_1kb_parsed_peve.txt
Redoing Peve as of 10/30/24 - adding gene ids to 3’UTR fasta and more stringent cutoffs for miranda
cd /data/putnamlab/jillashey/genome/Peve
module load BEDTools/2.30.0-GCC-11.3.0
awk '{print $1 "\t" $4-1 "\t" $5 "\t" $9 "\t" "." "\t" $7}' peve.GFFannotation.3UTR_1kb_corrected.gff | sed 's/"//g' > peve.GFFannotation.3UTR_1kb_corrected.bed
bedtools getfasta -fi Porites_evermanni_v1.fa -bed peve.GFFannotation.3UTR_1kb_corrected.bed -fo peve_3UTR_1kb.fasta -name
Rerun miranda with -en -20 -strict and the rest as defaults. Submitted batch job 346029
counting number of putative interactions predicted Wed Oct 30 12:23:23 EDT 2024
1789400
Parsing output Wed Oct 30 12:23:42 EDT 2024
counting number of putative interactions predicted Wed Oct 30 12:23:42 EDT 2024
7187 /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_peve.txt
Pmea
aka Ptuahensis
To run miranda, I need to identify the 3’ UTR ends.
First, identify counts of each feature from gff file
cd /data/putnamlab/jillashey/genome/Pmea
grep -v '^#' Pocillopora_meandrina_HIv1.genes_sorted.gff3 | cut -s -f 3 | sort | uniq -c | sort -rn > all_features_pmea.txt
208535 exon
208535 CDS
31840 transcript
Generate individual gff for transcripts.
grep $'\ttranscript\t' Pocillopora_meandrina_HIv1.genes_sorted.gff3 > Pmea_transcript.gtf
Extract scaffold lengths
cat is Pocillopora_meandrina_HIv1.assembly.fasta | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' > Pmea.Chromosome_lengths.txt
wc -l Pmea.Chromosome_lengths.txt
212 Pmea.Chromosome_lengths.txt
Extract scaffold names
awk -F" " '{print $1}' Pmea.Chromosome_lengths.txt > Pmea.Chromosome_names.txt
Create 1kb 3’UTR in gff
interactive
module load BEDTools/2.30.0-GCC-11.3.0
bedtools flank -i Pmea_transcript.gtf -g Pmea.Chromosome_lengths.txt -l 0 -r 1000 -s | awk '{gsub("transcript","3prime_UTR",$3); print $0 }' | awk '{if($5-$4 > 3)print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9}' | tr ' ' '\t' > Pmea_3UTR_1kb.gtf
Subtract portions of 3’UTRs that overlap nearby genes
bedtools subtract -a Pmea_3UTR_1kb.gtf -b Pmea_transcript.gtf > Pmea_3UTR_1kb_corrected.gtf
Extract 3’UTR sequences from genome
awk '{print $1 "\t" $4-1 "\t" $5 "\t" $9 "\t" "." "\t" $7}' Pmea_3UTR_1kb_corrected.gtf | sed 's/"//g' > Pmea_3UTR_1kb_corrected.bed
bedtools getfasta -fi Pocillopora_meandrina_HIv1.assembly.fasta -bed Pmea_3UTR_1kb_corrected.bed -fo Pmea_3UTR_1kb.fasta -name
Run miranda for Pmea data. In the scripts folder: nano miranda_strict_all_1kb_pmea.sh
#!/bin/bash -i
#SBATCH -t 48:00:00
#SBATCH --nodes=1 --ntasks-per-node=10
#SBATCH --export=NONE
#SBATCH --mem=500GB
#SBATCH --mail-type=BEGIN,END,FAIL #email you when job starts, stops and/or fails
#SBATCH --mail-user=jillashey@uri.edu #your email to send notifications
#SBATCH --account=putnamlab
#SBATCH -D /data/putnamlab/jillashey/e5/scripts
#SBATCH -o slurm-%j.out
#SBATCH -e slurm-%j.error
echo "PMEA aka PTUH starting miranda run with all genes and miRNAs with energy cutoff <-20 and strict binding invoked"$(date)
module load Miniconda3/4.9.2
conda activate /data/putnamlab/conda/miranda
miranda /data/putnamlab/jillashey/e5/mirna_seqs/Ptuh_results_mature_named.fasta /data/putnamlab/jillashey/genome/Pmea/Pmea_3UTR_1kb.fasta -en -20 -strict -out /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_ptuh.tab
conda deactivate
echo "miranda run finished!"$(date)
echo "counting number of putative interactions predicted" $(date)
zgrep -c "Performing Scan" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_ptuh.tab
echo "Parsing output" $(date)
grep -A 1 "Scores for this hit:" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_ptuh.tab | sort | grep '>' > /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_ptuh.txt
echo "counting number of putative interactions predicted" $(date)
wc -l /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_ptuh.txt
echo "PMEA aka PTUH miranda script complete" $(date)
Submitted batch job 346032. Results:
counting number of putative interactions predicted Wed Oct 30 12:42:23 EDT 2024
1204979
Parsing output Wed Oct 30 12:42:34 EDT 2024
counting number of putative interactions predicted Wed Oct 30 12:42:35 EDT 2024
3863 /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_ptuh.txt
Written on June 15, 2024