Commit 168e616f authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
Browse files

Update all_species_F_M_Wsnps.md

parent e348984e
......@@ -10,21 +10,41 @@ working directory: `/nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_
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)
```
bam_to_fastq
module load picard
cd /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/
java -jar /nfs/scistore03/vicosgrp/Bioinformatics_2021_temp/Reads/Programs/picard.jar SamToFastq I=/archive3/group/vicosgrp/artemia_RNAseq_reads/ArtemiaSinica/39897_CCGTCC_C9HBBANXX_5_20160809B_20160809.bam F=A.sinica.F.head.RNA.97_1.fq F2=A.sinica.F.head.RNA.97_2.fq
java -jar /nfs/scistore03/vicosgrp/ukhaurat/programs/picard.jar SamToFastq I=A.sinica_F_head_RNA_97.bam F=A_97_1.fq F2=A_97_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/39898_GCCAAT_C9HBBANXX_5_20160809B_20160809.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.F.head.RNA.98_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.F.head.RNA.98_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/40769_ACTGAT_C9MF6ANXX_1_20160830B_20160830.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.F.head.RNA.69_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.F.head.RNA.69_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/40770_GTCCGC_C9MF6ANXX_1_20160830B_20160830.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.F.head.RNA.70_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.F.head.RNA.70_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/39901_TGACCA_C9HBBANXX_5_20160809B_20160809.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.M.head.RNA.01_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.M.head.RNA.01_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaSinica/39902_ACTGAT_C9HBBANXX_5_20160809B_20160809.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.M.head.RNA.02_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.sinica.M.head.RNA.02_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/Kazakhstan/41809_GATCAG_C9M9GANXX_7_20161014B_20161014.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.kazakhstan.F.head.RNA.09_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.kazakhstan.F.head.RNA.09_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/Kazakhstan/41810_CGTACG_C9M9GANXX_7_20161014B_20161014.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.kazakhstan.F.head.RNA.10_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.kazakhstan.F.head.RNA.10_2.fq
scp -o ProxyJump=ukhaurat@login.ist.ac.at /Users/ukhaurat/Downloads/picard.jar ukhaurat@bea81:/nfs/scistore03/vicosgrp/ukhaurat/programs/
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/Kazakhstan/41803_ACAGTG_C9MF6ANXX_1_20160830B_20160830.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.kazakhstan.M.head.RNA.03_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.kazakhstan.M.head.RNA.03_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/Kazakhstan/41804_GGCTAC_C9MF6ANXX_1_20160830B_20160830.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.kazakhstan.M.head.RNA.04_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.kazakhstan.M.head.RNA.04_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaUrmiana/61775_AGCGATAGTAATCTTA_CC1HJANXX_3_20180406B_20180406.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.urmiana.F.head.RNA.75_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.urmiana.F.head.RNA.75_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaUrmiana/61779_ATTCAGAAATAGAGGC_CC1HJANXX_2_20180406B_20180406.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.urmiana.F.head.RNA.79_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.urmiana.F.head.RNA.79_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaUrmiana/61773_TCCGCGAAGGCTCTGA_CC1HJANXX_3_20180406B_20180406.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.urmiana.M.head.RNA.73_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.urmiana.M.head.RNA.73_2.fq
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/ArtemiaUrmiana/61777_TCCGGAGAGTACTGAC_CC1HJANXX_2_20180406B_20180406.bam -F /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.urmiana.M.head.RNA.77_1.fq -F2 /nfs/scistore03/vicosgrp/ukhaurat/all_species_males_females_Wsnps/A.urmiana.M.head.RNA.77_2.fq
sbatch bam_to_fastq.sh
Submitted batch job 24691174
Submitted batch job 24692864
A.sinica_F_head_RNA_97.bam
A.sinica_F_head_RNA_69.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
......@@ -34,7 +54,6 @@ 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
......@@ -43,6 +62,7 @@ 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
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment