Put the following commands into a new file called "commands" using nano. | Code Block |
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| title | Example commands file |
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| breseq -j 3 -r NC_012967.1.gbk -o output_00K SRR030252_1.fastq SRR030252_2.fastq &> 00K.log.txt &
breseq -j 3 -r NC_012967.1.gbk -o output_02K SRR030253_1.fastq SRR030253_2.fastq &> 02K.log.txt &
breseq -j 3 -r NC_012967.1.gbk -o output_05K SRR030254_1.fastq SRR030254_2.fastq &> 05K.log.txt &
breseq -j 3 -r NC_012967.1.gbk -o output_10K SRR030255_1.fastq SRR030255_2.fastq &> 10K.log.txt &
breseq -j 3 -r NC_012967.1.gbk -o output_15K SRR030256_1.fastq SRR030256_2.fastq &> 15K.log.txt &
breseq -j 3 -r NC_012967.1.gbk -o output_20K SRR030257_1.fastq SRR030257_2.fastq &> 20K.log.txt &
breseq -j 3 -r NC_012967.1.gbk -o output_40K SRR030258_1.fastq SRR030258_2.fastq &> 40K.log.txt &
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| Code Block |
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| title | how to execute all the commands at once |
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| chmod +x commands # makes the commands file executable
./commands # executes the commands file |
This will take several minutes to finish, making it a good opportunity to go back through some of the more detailed information in the ls5 and linux tutorial from earlier, and interrogate the output from the lambda phage data. |