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This should also go pretty fast: you . You can see the resulting files using ls like before.
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cd $SCRATCH/core_ngs/alignment ln -s -f $WORK/core_ngs/references/bt2/vibCho vibCho |
In the previous exercise, we set specific local alignment parameters for bowtie2 that took into account the fact that the dataset was derived from small RNA. However, in this case the Note that here the data is from standard mRNA sequencing, meaning that the DNA fragments are typically longer than the reads. There There is likely to be very little contamination that would require using a local rather than global alignment, or many other pre-processing steps (e.g. adapter trimming). ThusThus, we will run bowtie2 with default parameters, omitting any options other than the input, output, and reference index. The The command would look like this:
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Create a commands file called bt2_vibCho.cmds with this task definition then generate and submit a batch job for it (time 1 hour, normal development queue).
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Use nano to create the bt2_vibCho.cmds file. Then:
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When the job is complete you should have a cholera_rnaseq.sam file that you can examine using whatever commands you like. In the past two exercises, we have In the previous exercise we explored a few different sorts of commands that you might run on this file to get different sorts kinds of information. Those Those commands will provide similar information here , since this file is also in SAM/BAM format. In In the last exercise, we will come back to this SAM file (and the others) to explore ways to compress them effectively and to extract basic quality statistics.
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