Commit e348984e authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
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Update all_species_F_M_Wsnps.md

parent 81653f0e
......@@ -3,6 +3,8 @@
We want to check for W-SNPs in males and females of different species. We will use RNA from heads of males and female. It will allow to have a representation how sex chromosomes are different in A.sinica, A.franciscana, A.urmiana, and A.kazakhastan and how the level of differentiation is different in them.
We will also check for W-SNPs in parthenogenetic (asexual) species which is going to prove they have the same sex chromosomes.
working directory: `/nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps`
## 1. Transform raw bam files into fasta
Location of all the raw reads [Beatriz's table](https://git.ist.ac.at/bvicoso/artemia_zw_sexasex_2020/-/blob/master/UsefulData_July2021.md#rna-seq-data-head)
......@@ -10,19 +12,19 @@ Location of all the raw reads [Beatriz's table](https://git.ist.ac.at/bvicoso/ar
```
module load picard
cd /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/
java -jar /nfs/scistore03/vicosgrp/Bioinformatics_2017/Reads/Programs/picard.jar SamToFastq SamToFastq I=A.sinica_F_head_RNA_97.bam F=A.sinica_F_head_RNA_97_1.fq F2=A.sinica_F_head_RNA_97_2.fq
java -jar /nfs/scistore03/vicosgrp/Bioinformatics_2021_temp/Reads/Programs/picard.jar SamToFastq I=/archive3/group/vicosgrp/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
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.sinica_F_head_RNA_69.bam
java -jar /nfs/scistore03/vicosgrp/ukhaurat/programs/picard.jar SamToFastq I=A.sinica_F_head_RNA_97.bam F=A_97_1.fq F2=A_97_2.fq
scp -o ProxyJump=ukhaurat@login.ist.ac.at /Users/ukhaurat/Downloads/picard.jar ukhaurat@bea81:/nfs/scistore03/vicosgrp/ukhaurat/programs/
sbatch bam_to_fastq.sh
Submitted batch job 24691174
A.sinica_F_head_RNA_97.bam
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
......@@ -32,9 +34,39 @@ 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
```
Trimming
```
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
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
${base}_1.fq ${base}_2.fq
${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
```
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