Commit e96f57e1 authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
Browse files

Update all_species_F_M_Wsnps.md

parent a0a1e4a0
......@@ -96,6 +96,8 @@ A.urmiana.M.head.RNA.73_1.fq
A.urmiana.M.head.RNA.73_2.fq
A.urmiana.M.head.RNA.77_1.fq
A.urmiana.M.head.RNA.77_2.fq
A.urmiana.F.head.RNA.75_1.fq
A.urmiana.F.head.RNA.75_2.fq
```
Trimming
......@@ -115,8 +117,10 @@ ILLUMINACLIP:/nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/Tri
SLIDINGWINDOW:4:22 MINLEN:36 LEADING:3 TRAILING:3
done
#delete tabs and enters!
/usr/bin/time -v sbatch trimming.sh
Submitted batch job 24698444
Submitted batch job 24751597
```
```
module load trimmomatic
......@@ -129,4 +133,16 @@ srun java -jar /nfs/scistore03/vicosgrp/Bioinformatics_2018/Beatriz/0-Software/T
/usr/bin/time -v sbatch trimming_gz.sh
Submitted batch job 24698471
```
Mapping
```
module load star
cd /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/
for f in /nfs/scistore03/vicosgrp/ukhaurat/all.species.males.females.Wsnps/*.fq
do base=$(basename ${f%%_*}) STAR --genomeDir /nfs/scistore03/vicosgrp/ukhaurat/full_assembly_analysis/index/ --readFilesIn ${base}_1.trim.fq ${base}_2.trim.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${f/.fq/_mapped} --runThreadN 10
done
sbatch star.sh
Submitted batch job 24754632
```
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