Commit 81653f0e authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
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Update all_species_F_M_Wsnps.md

parent a6bee657
......@@ -6,3 +6,35 @@ We will also check for W-SNPs in parthenogenetic (asexual) species which is goin
## 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)
```
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
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
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
```
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