Commit 348b2e46 authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
Browse files

Update all_species_F_M_Wsnps.md

parent e5f3ee4b
......@@ -54,50 +54,6 @@ java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_r
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/Atanasovsko/45192_GTCCGC_C9KRJANXX_7_20161102B_20161102.bam -F A.parAta.F.head.RNA.92_1.fq -F2 A.parAta.F.head.RNA.92_2.fq +
A.kazakhstan.F.head.RNA.09_1.fq
A.kazakhstan.F.head.RNA.09_2.fq
A.kazakhstan.F.head.RNA.10_1.fq
A.kazakhstan.F.head.RNA.10_2.fq
A.kazakhstan.M.head.RNA.03_1.fq
A.kazakhstan.M.head.RNA.03_2.fq
A.kazakhstan.M.head.RNA.04_1.fq
A.kazakhstan.M.head.RNA.04_2.fq
A.parAibi.F.head.RNA.424_1.fq
A.parAibi.F.head.RNA.424_2.fq
A.parAibi.F.head.RNA.425_1.fq
A.parAibi.F.head.RNA.425_2.fq
A.parAta.F.head.RNA.91_1.fq
A.parAta.F.head.RNA.91_2.fq
A.parAta.F.head.RNA.92_1.fq
A.parAta.F.head.RNA.92_2.fq
A.parUrm.F.head.RNA.56_1.fq
A.parUrm.F.head.RNA.56_2.fq
A.parUrm.F.head.RNA.57_1.fq
A.parUrm.F.head.RNA.57_2.fq
A.sinica.M.head.RNA.77_1.fasta.gz
A.sinica.M.head.RNA.77_2.fasta.gz
A.sinica.M.head.RNA.78_1.fasta.gz
A.sinica.M.head.RNA.78_2.fasta.gz
A.sinica.F.head.RNA.69_1.fq
A.sinica.F.head.RNA.69_2.fq
A.sinica.F.head.RNA.70_1.fq
A.sinica.F.head.RNA.70_2.fq
A.sinica.F.head.RNA.97_1.fq
A.sinica.F.head.RNA.97_2.fq
A.sinica.F.head.RNA.98_1.fq
A.sinica.F.head.RNA.98_2.fq
A.sinica.M.head.RNA.01_1.fq
A.sinica.M.head.RNA.01_2.fq
A.sinica.M.head.RNA.02_1.fq
A.sinica.M.head.RNA.02_2.fq
A.urmiana.F.head.RNA.79_1.fq
A.urmiana.F.head.RNA.79_2.fq
A.urmiana.M.head.RNA.73_1.fq
A.urmiana.M.head.RNA.73_2.fq
A.urmiana.M.head.RNA.77_1.fq
A.urmiana.M.head.RNA.77_2.fq
A.urmiana.F.head.RNA.75_1.fq
A.urmiana.F.head.RNA.75_2.fq
```
Trimming
......@@ -139,13 +95,6 @@ Mapping
module load star
cd /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/
for f in /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/*.fq
do base=$(basename ${f%%_*}) STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn ${base}_1.trim.fq ${base}_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${f/.fq/_mapped} --runThreadN 10
done
sbatch star.sh
Submitted batch job 24754632
```
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.kazakhstan.F.head.RNA.10_1.trim.fq A.kazakhstan.F.head.RNA.10_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.kazakhstan.F.head.RNA.10_ --runThreadN 10
......@@ -153,27 +102,22 @@ STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.kazakhstan.M.head.RNA.04_1.trim.fq A.kazakhstan.M.head.RNA.04_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.kazakhstan.M.head.RNA.04_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.parAibi.F.head.RNA.424_1.trim.fq A.parAibi.F.head.RNA.424_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.parAibi.F.head.RNA.424_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.parAibi.F.head.RNA.425_1.trim.fq A.parAibi.F.head.RNA.425_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.parAibi.F.head.RNA.425_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.parAta.F.head.RNA.91_1.trim.fq A.parAta.F.head.RNA.91_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.parAta.F.head.RNA.91_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.parAta.F.head.RNA.92_1.trim.fq A.parAta.F.head.RNA.92_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.parAta.F.head.RNA.92_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.parUrm.F.head.RNA.56_1.trim.fq A.parUrm.F.head.RNA.56_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.parUrm.F.head.RNA.56_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.parUrm.F.head.RNA.57_1.trim.fq A.parUrm.F.head.RNA.57_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.parUrm.F.head.RNA.57_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.sinica.M.head.RNA.77_1.trim.fq A.sinica.M.head.RNA.77_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.sinica.M.head.RNA.77_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.sinica.M.head.RNA.78_1.trim.fq A.sinica.M.head.RNA.78_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.sinica.M.head.RNA.78_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.sinica.F.head.RNA.69_1.trim.fq A.sinica.F.head.RNA.69_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.sinica.F.head.RNA.69_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.sinica.F.head.RNA.70_1.trim.fq A.sinica.F.head.RNA.70_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.sinica.F.head.RNA.70_ --runThreadN 10
......@@ -182,8 +126,6 @@ STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.sinica.F.head.RNA.98_1.trim.fq A.sinica.F.head.RNA.98_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.sinica.F.head.RNA.98_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.sinica.M.head.RNA.01_1.trim.fq A.sinica.M.head.RNA.01_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.sinica.M.head.RNA.01_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.sinica.M.head.RNA.02_1.trim.fq A.sinica.M.head.RNA.02_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.sinica.M.head.RNA.02_ --runThreadN 10
......@@ -196,5 +138,53 @@ STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn A.urmiana.F.head.RNA.75_1.trim.fq A.urmiana.F.head.RNA.75_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/A.urmiana.F.head.RNA.75_ --runThreadN 10
```
### SNP calling
```
module load samtools
module load bcftools
module load vcftools
cd /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/
#Call SNPs from the BAM alignments
srun bcftools mpileup -a AD,DP,SP -Ou -f CHRR_integrated.fa A.sinica.F.head.RNA.69_Aligned.sortedByCoord.out.bam A.sinica.F.head.RNA.70_Aligned.sortedByCoord.out.bam A.sinica.F.head.RNA.97_Aligned.sortedByCoord.out.bam A.sinica.F.head.RNA.98_Aligned.sortedByCoord.out.bam A.sinica.M.head.RNA.01_Aligned.sortedByCoord.out.bam A.sinica.M.head.RNA.02_Aligned.sortedByCoord.out.bam A.sinica.M.head.RNA.77_Aligned.sortedByCoord.out.bam A.sinica.M.head.RNA.78_Aligned.sortedByCoord.out.bam A.kazakhstan.F.head.RNA.09_Aligned.sortedByCoord.out.bam A.kazakhstan.F.head.RNA.10_Aligned.sortedByCoord.out.bam A.kazakhstan.M.head.RNA.03_Aligned.sortedByCoord.out.bam A.kazakhstan.M.head.RNA.04_Aligned.sortedByCoord.out.bam A.urmiana.F.head.RNA.75_Aligned.sortedByCoord.out.bam A.urmiana.F.head.RNA.79_Aligned.sortedByCoord.out.bam A.urmiana.M.head.RNA.73_Aligned.sortedByCoord.out.bam A.urmiana.M.head.RNA.77_Aligned.sortedByCoord.out.bam A.parAta.F.head.RNA.91_Aligned.sortedByCoord.out.bam A.parAta.F.head.RNA.92_Aligned.sortedByCoord.out.bam A.parAibi.F.head.RNA.424_Aligned.sortedByCoord.out.bam A.parAibi.F.head.RNA.425_Aligned.sortedByCoord.out.bam A.parUrm.F.head.RNA.56_Aligned.sortedByCoord.out.bam A.parUrm.F.head.RNA.57_Aligned.sortedByCoord.out.bam| bcftools call -v -f GQ,GP -mO z -o head.sin.kaz.urm_vcf.gz
#filter for quality and coverage
srun vcftools --gzvcf head.sin.kaz.urm_vcf.gz --remove-indels --maf 0.1 --max-missing 0.9 --minQ 30 --min-meanDP 10 --max-meanDP 100 --minDP 10 --maxDP 100 --recode --stdout > head.sin.kaz.urm_filtered.vcf
#Filter 2: remove multiallelic
#bcftools view --max-alleles 2 --exclude-types indels head_asex_raremale_cov5_filtered.vcf > head_asex_raremale_cov5_filtered2.vcf
```
sbatch snp_calling_sin.kaz.urm.sh
Submitted batch job 24779195
1. A.sinica.F.head.RNA.69_Aligned.sortedByCoord.out.bam
2. A.sinica.F.head.RNA.70_Aligned.sortedByCoord.out.bam
3. A.sinica.F.head.RNA.97_Aligned.sortedByCoord.out.bam
4. A.sinica.F.head.RNA.98_Aligned.sortedByCoord.out.bam
5. A.sinica.M.head.RNA.01_Aligned.sortedByCoord.out.bam
6. A.sinica.M.head.RNA.02_Aligned.sortedByCoord.out.bam
7. A.sinica.M.head.RNA.77_Aligned.sortedByCoord.out.bam
8. A.sinica.M.head.RNA.78_Aligned.sortedByCoord.out.bam
9. A.kazakhstan.F.head.RNA.09_Aligned.sortedByCoord.out.bam
10. A.kazakhstan.F.head.RNA.10_Aligned.sortedByCoord.out.bam
11. A.kazakhstan.M.head.RNA.03_Aligned.sortedByCoord.out.bam
12. A.kazakhstan.M.head.RNA.04_Aligned.sortedByCoord.out.bam
13. A.urmiana.F.head.RNA.75_Aligned.sortedByCoord.out.bam
14. A.urmiana.F.head.RNA.79_Aligned.sortedByCoord.out.bam
15. A.urmiana.M.head.RNA.73_Aligned.sortedByCoord.out.bam
16. A.urmiana.M.head.RNA.77_Aligned.sortedByCoord.out.bam
17. A.parAta.F.head.RNA.91_Aligned.sortedByCoord.out.bam
18. A.parAta.F.head.RNA.92_Aligned.sortedByCoord.out.bam
19. A.parAibi.F.head.RNA.424_Aligned.sortedByCoord.out.bam
20. A.parAibi.F.head.RNA.425_Aligned.sortedByCoord.out.bam
21. A.parUrm.F.head.RNA.56_Aligned.sortedByCoord.out.bam
22. A.parUrm.F.head.RNA.57_Aligned.sortedByCoord.out.bam
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