running miranda on updated mirnas for e5

JillAshey · Nov 3, 2024 · 6637839 · 6637839
1 parent fbc5ece
commit 6637839
Show file tree

Hide file tree

Showing 3 changed files with 314 additions and 0 deletions.
diff --git a/_posts/2024-10-01-October-2024-Goals.md b/_posts/2024-10-01-October-2024-Goals.md
@@ -223,6 +223,49 @@ October 2024 goals and daily notebook entries.
 - Species comparisons for shared mirnas 
 - Resubmitted Astrangia review 
 
+## October reflection
+
+How did I do with my goals for this month? 
+
+### Writing and manuscripts 
+
+1. Dissertation proposal submission to grad school - done
+2. e5 ncRNA complete methods + results + outline of discussion - done for the most part. finishing up miRNA target results 
+3. Pacuta manuscript submission - nope but close to sending to coauthors for more edits 
+4. AST results for manuscript - nope
+5. JEB app - yes submitted
+6. EGRA - yes submitted
+7. Methods for Apul genome paper - done
+8. Resubmit Astrangia review to Biology Letters - done
+
+### Sample processing
+
+1. Re-amp 6 WGBS e5 deep dive samples - yes, still need to send
+2. Phys stuff for AST and Mcap DT - nope
+3. Find and send DNA for e5 samples - done
+
+### Data analysis
+
+1. 3'UTR for AST 2021 (GENE EXT) and rerun miRanda with that info - can move forward
+2. Run mirtarrnaseq for AST - no but can move forward
+3. Run mirtarrnaseq for deep dive (Apul) - no but have all miranda data for this project
+4. Mcap DT 2023 mRNA + miRNA counts matrix - yes for mRNA
+5. Compiling all phys stuff for AST 2021 - nope
+
+### Field work / travel 
+
+1. Figure out travel for cbass workshop - chat w/ Sofia - kinda? flights booked
+2. Apply for travel $$$ for cbass workshop - yes
+3. Apply for travel $$$ for sicb - yes 
+
+This was a very busy month and a lot of my data analysis goals got thrown off by revisions to the Astrangia review. I did get a lot of writing done! And several apps are submitted for travel support. 
+
+
+
+
+
+
+
 to do 
 
 - HI job app 

diff --git a/_posts/2024-11-01-November-2024-Goals.md b/_posts/2024-11-01-November-2024-Goals.md
@@ -0,0 +1,56 @@
+---
+layout: post
+title: October 2024 Goals
+date: '2024-10-01'
+categories: Monthly_Goals
+tags: Goals
+---
+
+October 2024 goals and daily notebook entries.
+
+## Goals  
+
+### Writing and manuscripts 
+
+1. e5 ncRNA complete draft of manuscript 
+2. Pacuta manuscript send to coauthors for edits 
+3. AST results for manuscript 
+
+### Sample processing
+
+1. Send WGBS e5 deep dive samples 
+2. Phys stuff for AST and Mcap DT
+
+### Data analysis
+
+1. Make fasta for 3'UTRs with gene names and rerun miranda 
+2. Run mirtarrnaseq for AST and make figures for manuscript 
+3. Run mirtarrnaseq for deep dive (Apul) - need count matrices for both miRNA and mRNA and miranda info 
+4. Figure out trimming for miRNA data Mcap DT 2023 
+5. Compiling all phys stuff for AST 2021 (if time)
+
+### Field work / travel 
+
+1. Resgister for sicb 
+2. Book flights for sicb 
+3. Confirm travel for cbass workshop
+
+## Daily log 
+
+### 20241101
+
+- e5 ncRNA paper writing 
+- e5 meeting 
+- 
+
+
+
+
+
+
+
+to do 
+
+- HI job app 
+- Lirman lab job app 
+- pacuta discussion
diff --git a/_posts/2024-11-01-e5-deepdive-TargetPrediction-Updated-miRNAs.md b/_posts/2024-11-01-e5-deepdive-TargetPrediction-Updated-miRNAs.md
@@ -0,0 +1,215 @@
+---
+layout: post
+title: e5 closest
+date: '2024-11-01'
+categories: Analysis
+tags: [Bioinformatics]
+projects: e5 deep dive
+---
+
+## e5 deep dive expression - miRNA target prediction 
+
+I am redoing the miRNA target prediction analysis for the deep dive expression project. Kathleen reran the miRNA short stack with a different version of the software and the results changed slightly (see [issue](https://github.com/urol-e5/deep-dive-expression/issues/3)). 
+
+For miRNA target prediction, the 3'UTR sequences of the genes are needed. These typically aren't annotated in coral genomes but I manually added them by adding 1000bp to the right flank of the gene and subtracting any overlap with nearby genes (see [post](https://github.com/JillAshey/JillAshey_Putnam_Lab_Notebook/blob/master/_posts/2024-06-15-e5-deepdive-miRNA-TargetPrediction.md)). I already have the 3'UTR sequences for our species of interest woohoo. Download updated miRNA sequences onto Andromeda for target prediction with miranda software. 
+
+Note - miRNA sequences are not named yet as of 11/1/24. 
+
+### Apulchra 
+
+Download new sequences and rename fasta files. Copied fasta sequences from [here](https://github.com/urol-e5/deep-dive-expression/blob/main/D-Apul/output/11-Apul-sRNA-ShortStack_4.1.0-pulchra_genome/ShortStack_out/mir.fasta). 
+
+```
+cd /data/putnamlab/jillashey/e5/mirna_seqs
+nano Apul_updated_results.fasta # paste fasta sequences 
+grep -A 1 'mature' Apul_updated_results.fasta | grep -v '^--$' > Apul_updated_results_mature.fasta
+
+zgrep -c ">" Apul_updated_results_mature.fasta
+39
+```
+
+In original run (using old short stack version and Amil genome), 38 mature miRNAs were identified. With updated short stack and new Apul genome, 39 mature miRNAs were identified. 
+
+I already have the 3'UTR fasta file here: `/data/putnamlab/jillashey/e5/refs/Apul/Apul_3UTR_1kb.fasta`. In the scripts folder: `nano miranda_strict_all_1kb_apul_updated.sh`
+
+```
+#!/bin/bash -i
+#SBATCH -t 48:00:00
+#SBATCH --nodes=1 --ntasks-per-node=10
+#SBATCH --export=NONE
+#SBATCH --mem=500GB
+#SBATCH --mail-type=BEGIN,END,FAIL #email you when job starts, stops and/or fails
+#SBATCH [email protected] #your email to send notifications
+#SBATCH --account=putnamlab
+#SBATCH -D /data/putnamlab/jillashey/e5/scripts
+#SBATCH -o slurm-%j.out
+#SBATCH -e slurm-%j.error
+
+echo "Apul starting miranda run with all genes and miRNAs with energy cutoff <-20 and strict binding invoked"$(date)
+echo "Using updated miRNAs from newer short stack version"
+
+module load Miniconda3/4.9.2
+conda activate /data/putnamlab/conda/miranda 
+
+miranda /data/putnamlab/jillashey/e5/mirna_seqs/Apul_updated_results_mature.fasta /data/putnamlab/jillashey/e5/refs/Apul/Apul_3UTR_1kb.fasta -en -20 -strict -out /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_apul_updated.tab
+
+conda deactivate
+
+echo "miranda run finished!"$(date)
+echo "counting number of interactions attempted" $(date)
+
+zgrep -c "Performing Scan" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_apul_updated.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_updated.txt
+
+echo "counting number of putative interactions predicted" $(date)
+wc -l /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_apul_updated.txt
+
+echo "Apul miranda script complete" $(date)
+```
+
+Submitted batch job 346351. Results: 
+
+```
+counting number of interactions attempted Fri Nov 1 14:02:45 EDT 2024
+2062788
+Parsing output Fri Nov 1 14:02:46 EDT 2024
+counting number of putative interactions predicted Fri Nov 1 14:02:46 EDT 2024
+6109 /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_apul_updated.txt
+```
+
+With previous miRNAs and Amil genome, there were 4144 putative interactions predicted. With updated miRNAs and Apul genome, 6109 putative interactions were predicted. 
+
+### Pevermanni 
+
+Download new sequences and rename fasta files. Copied fasta sequences from [here](https://github.com/urol-e5/deep-dive-expression/blob/main/E-Peve/output/05-Peve-sRNA-ShortStack_4.1.0/ShortStack_out/mir.fasta). 
+
+```
+cd /data/putnamlab/jillashey/e5/mirna_seqs
+nano Peve_updated_results.fasta # paste fasta sequences 
+grep -A 1 'mature' Peve_updated_results.fasta | grep -v '^--$' > Peve_updated_results_mature.fasta
+
+zgrep -c ">" Peve_updated_results_mature.fasta
+45
+```
+
+In original run (using old short stack version), 46 mature miRNAs were identified. With updated short stack, 45 mature miRNAs were identified. 
+
+I already have the 3'UTR fasta file here: `/data/putnamlab/jillashey/genome/Peve/peve_3UTR_1kb.fasta`. In the scripts folder: `nano miranda_strict_all_1kb_peve_updated.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 [email protected] #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 energy cutoff <-20 and strict binding invoked"$(date)
+echo "Using updated miRNAs from newer short stack version"
+
+module load Miniconda3/4.9.2
+conda activate /data/putnamlab/conda/miranda 
+
+miranda /data/putnamlab/jillashey/e5/mirna_seqs/Peve_updated_results_mature.fasta /data/putnamlab/jillashey/genome/Peve/peve_3UTR_1kb.fasta -en -20 -strict -out /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_peve_updated.tab
+
+conda deactivate
+
+echo "miranda run finished!"$(date)
+echo "counting number of interactions attempted" $(date)
+
+zgrep -c "Performing Scan" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_peve_updated.tab
+
+echo "Parsing output" $(date)
+grep -A 1 "Scores for this hit:" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_peve_updated.tab | sort | grep '>' > /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_peve_updated.txt
+
+echo "counting number of putative interactions predicted" $(date)
+wc -l /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_peve_updated.txt
+
+echo "Peve miranda script complete" $(date)
+```
+
+Submitted batch job 346352. Results: 
+
+```
+counting number of interactions attempted Fri Nov 1 14:05:10 EDT 2024
+1750500
+Parsing output Fri Nov 1 14:05:17 EDT 2024
+counting number of putative interactions predicted Fri Nov 1 14:05:17 EDT 2024
+5067 /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_peve_updated.txt
+```
+
+With previous miRNAs, there were 7187 putative interactions predicted. With updated miRNAs, 5067 putative interactions were predicted. 
+
+### Ptuahiniensis
+
+Download new sequences and rename fasta files. Copied fasta sequences from [here](https://github.com/urol-e5/deep-dive-expression/blob/main/F-Ptuh/output/05-Ptuh-sRNA-ShortStack_4.1.0/ShortStack_out/mir.fasta). 
+
+```
+cd /data/putnamlab/jillashey/e5/mirna_seqs
+nano Ptuh_updated_results.fasta # paste fasta sequences 
+grep -A 1 'mature' Ptuh_updated_results.fasta | grep -v '^--$' > Ptuh_updated_results_mature.fasta
+
+zgrep -c ">" Ptuh_updated_results_mature.fasta
+37
+```
+
+In original run (using old short stack version), 37 mature miRNAs were identified. With updated short stack, 37 mature miRNAs were identified. 
+
+I already have the 3'UTR fasta file here: `/data/putnamlab/jillashey/genome/Pmea/Pmea_3UTR_1kb.fasta`. In the scripts folder: `nano miranda_strict_all_1kb_ptuh_updated.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 [email protected] #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 "Ptuh starting miranda run with all genes and miRNAs with energy cutoff <-20 and strict binding invoked"$(date)
+echo "Using updated miRNAs from newer short stack version"
+
+module load Miniconda3/4.9.2
+conda activate /data/putnamlab/conda/miranda 
+
+miranda /data/putnamlab/jillashey/e5/mirna_seqs/Ptuh_updated_results_mature.fasta /data/putnamlab/jillashey/genome/Pmea/Pmea_3UTR_1kb.fasta -en -20 -strict -out /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_ptuh_updated.tab
+
+conda deactivate
+
+echo "miranda run finished!"$(date)
+echo "counting number of interactions attempted" $(date)
+
+zgrep -c "Performing Scan" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_ptuh_updated.tab
+
+echo "Parsing output" $(date)
+grep -A 1 "Scores for this hit:" /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_ptuh_updated.tab | sort | grep '>' > /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_ptuh_updated.txt
+
+echo "counting number of putative interactions predicted" $(date)
+wc -l /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_ptuh_updated.txt
+
+echo "Peve miranda script complete" $(date)
+```
+
+Submitted batch job 346353. Results: 
+
+```
+counting number of interactions attempted Fri Nov 1 14:04:16 EDT 2024
+1204979
+Parsing output Fri Nov 1 14:04:19 EDT 2024
+counting number of putative interactions predicted Fri Nov 1 14:04:19 EDT 2024
+4105 /data/putnamlab/jillashey/e5/output/miranda/miranda_strict_all_1kb_parsed_ptuh_updated.txt
+```
+
+With previous miRNAs, there were 3863 putative interactions predicted. With updated miRNAs, 4105 putative interactions were predicted. 
+