Commit cedb58ed authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
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parent d17798e4
# Heterozygosity on the perfwct genome
For the paper Marwan improved the genome even better and now it is very good. So I want to redo heterozygosity on it.
First, I need to map the reads:
```
star_2.0.sh
module load star
cd /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/
STAR --runMode genomeGenerate --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --genomeFastaFiles /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/CHRR_integrated.fa --runThreadN 10 --genomeChrBinNbits 15
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn F2hybrid.female10_1.trim.fq F2hybrid.female10_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/F2hybrid.female10_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn asexualsister_Aibi_1_trimmed.fq asexualsister_Aibi_2_trimmed.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/asexualsister_Aibi_ --runThreadN 10
STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn raremale_Aibi_1_trimmed.fq raremale_Aibi_2_trimmed.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/raremale_Aibi_ --runThreadN 10
```
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