!!! Re-running the pipeline
\\
The pipeline strives to minimize the amount of work done. Each time it is run on the same dataset/accession_number with the exact same set of options, the pipeline will check at each step whether previous results, such alignment files, reports or expression estimates, already exist and if this is the case the results will be retrieved instead of being re-created. When re-running the pipeline with different options the results are stored in different directories. \\

!! Bypassing steps
! Providing your own alignment files
You can bypass the alignment step by setting the aligner to "custom", e.g.:
{{{
> e <- ArrayExpressHTS("E-GEOD-16190", options=list(aligner="custom") )
}}}
And by placing your SAM and BAM files in the correct directory of your project structure. This is under each run's subdirectory, e.g.:
{{{
E-GEOD-16190
|
|___ SRR017242
     |___ custom_alignment                    # place your file in this dir
           |___ accepted_hits.sam             # file has to be named accepted_hits.sam and be previously sorted 
           |                                  # with the following command:
           |                                  # sort -k 3,3 -k 4,4n accepted_hits.unsorted.sam > accepted_hits.sam
           |___ accepted_hits.bam             # file has to be names accepted_hits.bam
           |___ accepted_hits.sortednames.bam # file has to be named accepted_hits.sortednames.bam
}}}
! Disabling report generation
Disabling the report generation steps speeds up the processing of your experiment. This can be done by setting the appropriate options to the main function:
{{{
e <- ArrayExpressHTS("E-GEOD-16190", want.reports = FALSE )
}}}
or
{{{
e <- ArrayExpressHTSFastQ("E-GEOD-16190", want.reports = FALSE )
}}}
\\
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