Commit 1a1dcc02 authored by Uladzislava KHAURATOVICH's avatar Uladzislava KHAURATOVICH 💬
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Update all_species_F_M_Wsnps.md

parent 168e616f
......@@ -14,23 +14,20 @@ bam_to_fastq
module load picard
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/40770_GTCCGC_C9MF6ANXX_1_20160830B_20160830.bam -F A.sinica.F.head.RNA.70_1.fq -F2 A.sinica.F.head.RNA.70_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 A.sinica.M.head.RNA.01_1.fq -F2 A.sinica.M.head.RNA.01_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 A.sinica.M.head.RNA.02_1.fq -F2 A.sinica.M.head.RNA.02_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 A.kazakhstan.F.head.RNA.09_1.fq -F2 A.kazakhstan.F.head.RNA.09_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 A.kazakhstan.F.head.RNA.10_1.fq -F2 A.kazakhstan.F.head.RNA.10_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
java -jar $PICARD SamToFastq -I /archive3/group/vicosgrp/shared/artemia_RNAseq_reads/Kazakhstan/41803_ACAGTG_C9MF6ANXX_1_20160830B_20160830.bam -F A.kazakhstan.M.head.RNA.03_1.fq -F2 A.kazakhstan.M.head.RNA.03_2.fq +
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/Kazakhstan/41804_GGCTAC_C9MF6ANXX_1_20160830B_20160830.bam -F A.kazakhstan.M.head.RNA.04_1.fq -F2 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
......
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