Commit a0a1e4a0 authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
Browse files

Update all_species_F_M_Wsnps.md

parent fec34279
......@@ -14,8 +14,13 @@ bam_to_fastq
module load picard
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/40770_GTCCGC_C9MF6ANXX_1_20160830B_20160830.bam -F A.sinica.F.head.RNA.70_1.fq -F2 A.sinica.F.head.RNA.70_2.fq +
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/39897_CCGTCC_C9HBBANXX_5_20160809B_20160809.bam -F A.sinica.F.head.RNA.97_1.fq -F2 A.sinica.F.head.RNA.97_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/39898_GCCAAT_C9HBBANXX_5_20160809B_20160809.bam -F A.sinica.F.head.RNA.98_1.fq -F2 A.sinica.F.head.RNA.98_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/arartemia_RNAseq_reads/ArtemiaSinica/40769_ACTGAT_C9MF6ANXX_1_20160830B_20160830.bam -F A.sinica.F.head.RNA.69_1.fq -F2 A.sinica.F.head.RNA.69_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/40770_GTCCGC_C9MF6ANXX_1_20160830B_20160830.bam -F A.sinica.F.head.RNA.70_1.fq -F2 A.sinica.F.head.RNA.70_2.fq +
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/39901_TGACCA_C9HBBANXX_5_20160809B_20160809.bam -F A.sinica.M.head.RNA.01_1.fq -F2 A.sinica.M.head.RNA.01_2.fq +
......@@ -49,38 +54,48 @@ java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_r
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/Atanasovsko/45192_GTCCGC_C9KRJANXX_7_20161102B_20161102.bam -F A.parAta.F.head.RNA.92_1.fq -F2 A.parAta.F.head.RNA.92_2.fq +
A.sinica_F_head_RNA_69.bam
A.sinica_F_head_RNA_70.bam
A.sinica_F_head_RNA_97.bam
A.sinica_F_head_RNA_98.bam
A.sinica_M_head_RNA_01.bam
A.sinica_M_head_RNA_02.bam
A.sinica_M_head_RNA_77_1.fasta.gz
A.sinica_M_head_RNA_77_2.fasta.gz
A.sinica_M_head_RNA_78_1.fasta.gz
A.sinica_M_head_RNA_78_2.fasta.gz
A.urmiana_F_head_RNA_75.bam
A.urmiana_F_head_RNA_79.bam
A.urmiana_M_head_RNA_73.bam
A.urmiana_M_head_RNA_77.bam
A.kazakhstan_F_head_RNA_09.bam
A.kazakhstan_F_head_RNA_10.bam
A.kazakhstan_M_head_RNA_03.bam
A.kazakhstan_M_head_RNA_04.bam
A.parAibi_F_head_RNA_424.bam
A.parAibi_F_head_RNA_425.bam
A.parAta_F_head_RNA_91.bam
A.parAta_F_head_RNA_92.bam
A.parUrm_F_head_RNA_56.bam
A.parUrm_F_head_RNA_57.bam
A.kazakhstan.F.head.RNA.09_1.fq
A.kazakhstan.F.head.RNA.09_2.fq
A.kazakhstan.F.head.RNA.10_1.fq
A.kazakhstan.F.head.RNA.10_2.fq
A.kazakhstan.M.head.RNA.03_1.fq
A.kazakhstan.M.head.RNA.03_2.fq
A.kazakhstan.M.head.RNA.04_1.fq
A.kazakhstan.M.head.RNA.04_2.fq
A.parAibi.F.head.RNA.424_1.fq
A.parAibi.F.head.RNA.424_2.fq
A.parAibi.F.head.RNA.425_1.fq
A.parAibi.F.head.RNA.425_2.fq
A.parAta.F.head.RNA.91_1.fq
A.parAta.F.head.RNA.91_2.fq
A.parAta.F.head.RNA.92_1.fq
A.parAta.F.head.RNA.92_2.fq
A.parUrm.F.head.RNA.56_1.fq
A.parUrm.F.head.RNA.56_2.fq
A.parUrm.F.head.RNA.57_1.fq
A.parUrm.F.head.RNA.57_2.fq
A.sinica.F.head.RNA.77_1.fasta.gz
A.sinica.F.head.RNA.77_2.fasta.gz
A.sinica.M.head.RNA.78_1.fasta.gz
A.sinica.M.head.RNA.78_2.fasta.gz
A.sinica.F.head.RNA.69_1.fq
A.sinica.F.head.RNA.69_2.fq
A.sinica.F.head.RNA.70_1.fq
A.sinica.F.head.RNA.70_2.fq
A.sinica.F.head.RNA.97_1.fq
A.sinica.F.head.RNA.97_2.fq
A.sinica.F.head.RNA.98_1.fq
A.sinica.F.head.RNA.98_2.fq
A.sinica.M.head.RNA.01_1.fq
A.sinica.M.head.RNA.01_2.fq
A.sinica.M.head.RNA.02_1.fq
A.sinica.M.head.RNA.02_2.fq
A.urmiana.F.head.RNA.79_1.fq
A.urmiana.F.head.RNA.79_2.fq
A.urmiana.M.head.RNA.73_1.fq
A.urmiana.M.head.RNA.73_2.fq
A.urmiana.M.head.RNA.77_1.fq
A.urmiana.M.head.RNA.77_2.fq
```
Trimming
......@@ -90,7 +105,7 @@ module load trimmomatic
module load java
cd /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps
for f in /nfs/scistore03/vicosgrp/ukhaurat/proj/*_1.fq
for f in //nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/*_1.fq
do
base=$(basename ${f%%_*})
srun java -jar /nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 8
......@@ -99,13 +114,19 @@ ${base}_1.trim.fq ${base}_1un.trim.fq ${base}_2.trim.fq ${base}_2un.trim.fq
ILLUMINACLIP:/nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10
SLIDINGWINDOW:4:22 MINLEN:36 LEADING:3 TRAILING:3
done
/usr/bin/time -v sbatch trimming.sh
Submitted batch job 24698444
```
```
module load trimmomatic
cd /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/
scp -o ProxyJump=ukhaurat@login.ist.ac.at /Users/ukhaurat/Documents/full_assembly_analysis/heatmap_genome.R ukhaurat@bea81:/nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/
srun java -jar /nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 4 A.sinica.M.head.RNA.77_1.fasta.gz A.sinica.M.head.RNA.77_2.fasta.gz A.sinica.M.head.RNA.77_1_trimmed.fq A.sinica.M.head.RNA.77_1_un.trimmed.fq A.sinica.M.head.RNA.77_2_trimmed.fq A.sinica.M.head.RNA.77_2_un.trimmed.fq ILLUMINACLIP:/nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:22 MINLEN:36 LEADING:3 TRAILING:3
heatmap_genome.R
srun java -jar /nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 4 A.sinica.M.head.RNA.78_1.fasta.gz A.sinica.M.head.RNA.78_2.fasta.gz A.sinica.M.head.RNA.78_1_trimmed.fq A.sinica.M.head.RNA.78_1_un.trimmed.fq A.sinica.M.head.RNA.78_2_trimmed.fq A.sinica.M.head.RNA.78_2_un.trimmed.fq ILLUMINACLIP:/nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:22 MINLEN:36 LEADING:3 TRAILING:3
sbatch R_heatmap.sh
Submitted batch job 24694774
/usr/bin/time -v sbatch trimming_gz.sh
Submitted batch job 24698471
```
/usr/bin/time -v command
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