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First, we'll run breseq on a small data set to be sure that it is installed correctly, and to get a taste for what the output looks like. This sample is a mixed population of bacteriophage lambda that was co-evolved in lab with its E. coli hosts.
Data
| Note |
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| title | Possible errors on idev nodes |
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As mentioned yesterday, you can not copy from the BioITeam (because it is on corral-repl) while on an idev node. Logout of your idev session, copy the files, and be sure to start a new idev session as breseq should not be run on the headnode. |
The data files for this tutorial is located in following location:
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| language | bash |
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| title | By this point in the course you should not need to expand this box to see the suggested solution. You should continue expanding boxes such as this to make sure you are not drifting too far |
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| collapse | true |
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mkdir $SCRATCH/GVA_breseq_lambda_mixed_pop
cp $BI/ngs_course/lambda_mixed_pop/data/* $SCRATCH/GVA_breseq_lambda_mixed_pop |
| Note |
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| title | Possible errors on idev nodes |
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| As mentioned yesterday, you can not copy from the BioITeam (because it is on corral-repl) while on an idev node. Logout of your idev session, copy the files, and be sure to start a new idev session as breseq should not be run on the headnode. |
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| title | Now use the ls command to see what files were copied. again, you should not need to expand this to get the output listed below |
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| collapse | true |
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ls $SCRATCH/GVA_breseq_lambda_mixed_pop
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| language | bash |
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| title | breseq command |
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conda activate GVA-breseq
cd $SCRATCH/GVA_breseq_lambda_mixed_pop
breseq -j 6848 -r lambda.gbk lambda_mixed_population.fastq
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While breseq is running lets look at what the different parts of the command are actually doing:
| part | puprose |
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| -j 6848 | use 68 48 processors (recall we saw this was best in the rough testing using of bowtie2 |
| -r lambda.gbk | Use the lambda.gbk file as the reference to identify specific mutations |
| lambda_mixed_population.fastq | breseq assumes any argument not preceded by a - option to be an input fastq file to be used for mapping |
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| language | bash |
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| title | Commands to copy the input data from the first breseq run to a new folder, and rerun breseq on the same fastq and reference file in polymorphism mode. Since this copy command is between 2 scratch locations i doubt there will be issues with it, but remember to restart an idev node if you experience difficulties |
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mkdir $SCRATCH/GVA_breseq_lambda_mixed_pop_polymode
cp $SCRATCH/GVA_breseq_lambda_mixed_pop/lambda* $SCRATCH/GVA_breseq_lambda_mixed_pop_polymode
cd $SCRATCH/GVA_breseq_lambda_mixed_pop_polymode
breseq -j 6848 -p -r lambda.gbk lambda_mixed_population.fastq
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| language | bash |
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| title | As mentioned early in the course, some programs can actually take compressed fastq files in as input and breseq is 1 such program. In this example, breseq takes 2 fastq files, 1 as a non-compressed file, the other as a gzipped file. The command we want to run is: |
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breseq -j 6848 -r NC_012967.1.gbk SRR030257_1.fastq SRR030257_2.fastq.gz |
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Be sure that cat breseq_commands gives the following output exactly:
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breseq -j 6848 -r NC_012967.1.gbk SRR030257_1.fastq SRR030257_2.fastq.gz |
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