Commit 3601bc43 authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
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Update full_chromosome-level_assembly_analysis.md

parent 5859980b
......@@ -4,8 +4,8 @@ I want to repeat some analysis using a new genome assembly created by Marwan.
## 1. Map 20 hybrids RNA and their grandparents to the new genome.
Working directory: `/nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/`.
Genome: `/nfs/scistore03/vicosgrp/melkrewi/Project_confirm_genome_assembly/CHRR_integrated.fa`.
Working directory: `/nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/`.
Genome: `/nfs/scistore03/vicosgrp/melkrewi/Project_confirm_genome_assembly/CHRR_integrated.fa`.
Trimmed RNA reads from 20 hybrids and Kazakhstan and sinica grandparents: `/nfs/scistore03/vicosgrp/ukhaurat/dummyfather_proj/trimmed`.
- make links of files with trimmed reads
......@@ -398,12 +398,13 @@ filtered for
-i removed grep -v '\W2\W' -\_O-O_/- who knows what it is...
```
cat head_Gk1_Gs1_f_m_filtered2.vcf.simple | grep -v 'NA' | awk '($10 != "0" && $11 == "0")' | awk '( ($10+$11+$12+$13+$14+$15+$16+$17+$18+$19+$20+$21+$22+$23+$24+$25+$26+$27+$28+$29)>4 && ($10+$11+$12+$13+$14+$15+$16+$17+$18+$19+$20+$21+$22+$23+$24+$25+$26+$27+$28+$29)<16)' > head_Gk1_Gs1_f_m_filtered2.vcf.simple.filtered3
cat head_Gk1_Gs1_f_m_filtered2.vcf.simple | grep -v 'NA' | awk '($10 != "0" && $11 == "0")' | awk '{print $1, $2, $12, $13, $14, $15, $16, $17, $18, $19, $20, $21, $22, $23, $24, $25, $26, $27, $28, $29, $30, $31}' | grep -v '\W2\W' | awk '( ($3+$4+$5+$6+$7+$8+$9+$10+$11+$12+$13+$14+$15+$16+$17+$18+$19+$20+$21+$22)>4 && ($3+$4+$5+$6+$7+$8+$9+$10+$11+$12+$13+$14+$15+$16+$17+$18+$19+$20+$21+$22)<16)' > head_Gk1_Gs1_f_m_filtered2.vcf.simple.filtered
scp -o ProxyJump=ukhaurat@login.ist.ac.at ukhaurat@bea81:/nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/head_Gk1_Gs1_f_m_filtered2.vcf.simple.filtered3 /Users/ukhaurat/Documents/full_assembly_analysis
scp -o ProxyJump=ukhaurat@login.ist.ac.at ukhaurat@bea81:/nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/head_Gk1_Gs1_f_m_filtered2.vcf.simple.filtered /Users/ukhaurat/Documents/full_assembly_analysis
```
```
grep 'scaffold' head_Gk1_Gs1_f_m_filtered2.vcf.simple.filtered > head_Gk1_Gs1_f_m_filtered2.vcf.simple.filtered_scaffoldsplus
```
......
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