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Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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James A. Fellows Yates 2023-04-20 12:58:23 +02:00 committed by GitHub
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@ -255,13 +255,13 @@ This directory will be present and contain the unmapped reads from the `.fastq`
<summary>Output files</summary>
- `samtoolsstats`
- `<sample_id>_{fq,fastq}.gz`: Final reads that underwent preprocessing that were sent for classification/profiling.
- `<sample_id>_{fq,fastq}.gz`: Final reads that underwent preprocessing and were sent for classification/profiling.
</details>
The results directory will contain the 'final' processed reads used as input for classification/profiling. It will _only_ include the output of the \_last step of any combinations of preprocessing steps that may have been specified in the run configuration. For example, if you perform the read QC and host-removal preprocessing steps, the final reads that are sent to classification/profiling are the host-removed FASTQ files - this will be the ones present in this directory.
The results directory will contain the 'final' processed reads used as input for classification/profiling. It will _only_ include the output of the \_last step of any combinations of preprocessing steps that may have been specified in the run configuration. For example, if you perform the read QC and host-removal preprocessing steps, the final reads that are sent to classification/profiling are the host-removed FASTQ files - those will be the ones present in this directory.
> ⚠️ If you turn off all preprocessing steps, then no results will be present in this directory. This happens independtly for short- and long-reads. I.e. you will only have FASTQ files for short reads in this directory if you skip all long-read preprocessing.
> ⚠️ If you turn off all preprocessing steps, then no results will be present in this directory. This happens independently for short- and long-reads. I.e. you will only have FASTQ files for short reads in this directory if you skip all long-read preprocessing.
### SAMtools stats
@ -293,7 +293,7 @@ This is the last possible preprocessing step, so if you have multiple runs or li
Note that you will only find samples that went through the run merging step in this directory. For samples that had a single run or library will not go through this step of the pipeline and thus will not be present in this directory.
This directory and it's FASTQ files will only be present if you supply `--save_runmerged_reads`.Alternatively, if you wish only to have the 'final' reads that go into classification/profiling (i.e., that may have additional processing), do not specify this flag but rather specify `--save_analysis_ready_reads`, in which case the reads will be in the folder `analysis_ready_reads`.
This directory and its FASTQ files will only be present if you supply `--save_runmerged_reads`.Alternatively, if you wish only to have the 'final' reads that go into classification/profiling (i.e., that may have additional processing), do not specify this flag but rather specify `--save_analysis_ready_reads`, in which case the reads will be in the folder `analysis_ready_reads`.
### Bracken