Rui:Transfer and convert files
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Transfer and convert files[edit]
Transfer files[edit]
- Transfer files to genome-miner from meangenemachine
Transfer files to ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat: scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/tophat_Indx15/tophat_out/accepted_hits.bam ./Indx15_accepted_hits.bam scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/tophat_Indx14/tophat_out/accepted_hits.bam ./Indx14_accepted_hits.bam scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/tophat_Indx13/tophat_out/accepted_hits.bam ./Indx13_accepted_hits.bam scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/tophat_Indx12/tophat_out/accepted_hits.bam ./Indx12_accepted_hits.bam scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/tophat_Indx11/tophat_out/accepted_hits.bam ./Indx11_accepted_hits.bam scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/tophat_Indx10/tophat_out/accepted_hits.bam ./Indx10_accepted_hits.bam scp ruiliu@meangenemachine.dynamic.ucsd.edu:~/Hiseq111005/tophat_Indx5/tophat_out/accepted_hits.bam ./Indx5_accepted_hits.bam
- Transfer files from genome-miner to meangenemachine
ruiliu@meangenemachine-desktop:~/Hiseq111005/tophat_Indx9$ scp ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat/tophat_Indx9/* ./ scp ruiliu@genome-miner:~/RNAseq/Hiseq111005/tophat/tophat_Indx6/* ./
Convert files[edit]
- Convert bam to sam in genome-miner
samtools view -h Indx10_accepted_hits.bam > Indx10_accepted_hits.sam samtools view -h Indx11_accepted_hits.bam > Indx11_accepted_hits.sam nohup samtools view -h Indx12_accepted_hits.bam > Indx12_accepted_hits.sam & nohup samtools view -h Indx13_accepted_hits.bam > Indx13_accepted_hits.sam nohup samtools view -h Indx14_accepted_hits.bam > Indx14_accepted_hits.sam nohup samtools view -h Indx15_accepted_hits.bam > Indx15_accepted_hits.sam nohup samtools view -h Indx5_accepted_hits.bam > Indx5_accepted_hits.sam nohup samtools view -h Indx6_accepted_hits.bam > Indx6_accepted_hits.sam nohup samtools view -h Indx9_accepted_hits.bam > Indx9_accepted_hits.sam
- Convert bam to sam in meangenemachine
nohup samtools view -h ./tophat_Indx10/tophat_out/accepted_hits.bam > ./tophat_Indx10/tophat_out/accepted_hits.sam & nohup samtools view -h ./tophat_Indx11/tophat_out/accepted_hits.bam > ./tophat_Indx11/tophat_out/accepted_hits.sam & nohup samtools view -h ./tophat_Indx12/tophat_out/accepted_hits.bam > ./tophat_Indx12/tophat_out/accepted_hits.sam & nohup samtools view -h ./tophat_Indx13/tophat_out/accepted_hits.bam > ./tophat_Indx13/tophat_out/accepted_hits.sam & nohup samtools view -h ./tophat_Indx14/tophat_out/accepted_hits.bam > ./tophat_Indx14/tophat_out/accepted_hits.sam & nohup samtools view -h ./tophat_Indx15/tophat_out/accepted_hits.bam > ./tophat_Indx15/tophat_out/accepted_hits.sam & nohup samtools view -h ./tophat_Indx5/tophat_out/accepted_hits.bam > ./tophat_Indx5/tophat_out/accepted_hits.sam & nohup samtools view -h ./tophat_Indx6/tophat_out/accepted_hits.bam > ./tophat_Indx6/tophat_out/accepted_hits.sam & nohup samtools view -h ./tophat_Indx9/tophat_out/accepted_hits.bam > ./tophat_Indx9/tophat_out/accepted_hits.sam &