Commit 91e32133 authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
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Update !raremale_chromosome-level_assembly_analysis.md

parent 4edfe2e2
# Repeat the analysis for rare male sex chromosomes and it's asexual sister with the chromosome-level genome assembly
## 5. Map raremale DNA and its asexual sister to the new full genome
## 1. Map raremale DNA and its asexual sister to the new full genome
- make links of files with trimmed reads
cd /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/
......@@ -39,7 +39,37 @@ cat head_asex_raremale_cov5_filtered2.vcf | grep -v '^##' | perl -pi -e 's/:.*?\
```
why is it so big (100 858 148)? in comparisson with `head_Gk1_Gs1_f_m_filtered2.vcf_simple` (10 064 250 bytes). oh! probably it is because DNA was used.
### 6. Find SNPs with the lost heterozygosity in the raremale genome
## 2. Find W-SNPs and check for it in the raremale-asex VCF
What W and ZW SNPs we detected in the full-chromosonmal-level assembly?
`/nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis`
```
cat head_Gk1_Gs1_f_m_filtered2.vcf_simple.ZWassign | awk '{print $6}' | sort | uniq -c | awk '{print $2, $1}'
0 54841
1 181
2 820
```
181 W-SNPs, more than in the previous!
```
0 [autosome] 48673
1 [w] 144
2 [zw] 706
```
Prepare the list of W-SNP coordinates
```
cat w_snps_perl_script_full_assembly.txt | awk '{print $1, $2}' > w_snps_coordinates.txt
wc w_snps_coordinates.txt
| 181 362 2548 w_snps_coordinates.txt
```
Check for the W-SNPs in the raremale-asex VCF, we found 32 W-SNPs (last time it was 24)
```
grep -f w_snps_coordinates.txt head_asex_raremale_cov5_filtered2.vcf_simple > w_snps_raremale.txt
ukhaurat@bea81:~/full_assembly_analysis$ wc w_snps_raremale.txt
32 352 1142 w_snps_raremale.txt
```
## 3. Find SNPs with the lost heterozygosity in the raremale genome
```
# do it from the computer
......
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