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| Warning |
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| title | Submit to the TACC queue or run in an idev shell |
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Create a commands file and use launcher_creator.py followed by qsub. | Expand |
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| title | click here for a hint before getting the answer |
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| launcher_creator.py -h will give you insight to how to use that command. | Code Block |
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| | language | bash |
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| title | Click here for the specific launcher_creator.py commands |
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| collapse | true |
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| launcher_creator. py -n "bowtie2" --time 00:10:00| Code Block |
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| language | bash |
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| title | commands for the commands file if you can't work them out yourself |
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| collapse | true |
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| bowtie2 -t -x bowtie2/NC_012967.1 -1 SRR030257_1.fastq -2 SRR030257_2.fastq -S bowtie2/SRR030257.sam # the -t command is not required for the mapping, but it can be particularly informative when you begin comparing different mappers
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| Code Block |
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| language | bash |
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| title | Click here for the specific launcher_creator.py commands |
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| collapse | true |
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| launcher_creator.py -n "bowtie2" -t 00:10:00 |
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Your final output file is in SAM format. It's just a text file, so you can peek at it and see what it's like inside. Two warnings though:
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