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docs/output.md
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@ -107,7 +107,7 @@ Note that the FASTQ files may _not_ always be the 'final' reads that go into tax
</details>
The output logs are saved in the output folder and are part of MultiQC report.
The output logs are saved in the output folder and are part of MultiQC report.You do not normally need to check these manually.
We do **not** recommend using Porechop if you are already trimming the adapters with ONT's basecaller Guppy.
### BBDuk
@ -161,6 +161,8 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t
</details>
You can use the filtered FASTQ for other downstream analyses to reduce repeated preprocessing of files.
We do **not** recommend using Filtlong if you are performing filtering of low quality reads with ONT's basecaller Guppy.
### Bowtie2
@ -197,8 +199,8 @@ It is used with nf-core/taxprofiler to allow removal of 'host' (e.g. human) or o
</details>
By default, nf-core taxprofiler will provide the `.bam` file if host removal for long reads is turned on.
minimap2 is not yet supported as a module in MultiQC and therefore the alignment to host genome is reported via samtools stats in MultiQC report.
By default, nf-core taxprofiler will only provide the `.bam` file if host removal for long reads is turned on.
Note: minimap2 is not yet supported as a module in MultiQC and therefore there is no dedicated section in the MultiQC HTML. Rather, alignment statistics to host genome is reported via samtools stats module in MultiQC report.
### Samtools stats
@ -212,7 +214,7 @@ minimap2 is not yet supported as a module in MultiQC and therefore the alignment
</details>
Samtools output file is part of the MultiQC report and gives statistics about the mapped/unmapped reads to host reference genome.
In most cases you do not need to check this file, as it is rendered in the MultiQC run report.
### Bracken
@ -306,7 +308,7 @@ The main taxonomic classification files from Centrifuge are the `_combined_repor
</details>
The default taxonomic rank is `species`. You can provide a different one by updating the argument `--kaiju_taxon_rank`.
The most summary file is the `*combined_reports` file which summarises results across all samples. However if you wish to look at more precise information about each assignment, check the per-sample file. The default taxonomic rank is `species`. You can provide a different one by updating the argument `--kaiju_taxon_rank`.
### DIAMOND
@ -321,7 +323,7 @@ The default taxonomic rank is `species`. You can provide a different one by upda
</details>
You will receive the `*.sam` file if you provide the parameter `--diamond_save_reads` but in this case no taxonomic classification will be available, only the aligned reads in sam format.
By default you will receive a TSV output. Alternatively, you will receive a `*.sam` file if you provide the parameter `--diamond_save_reads` but in this case no taxonomic classification will be available(!), only the aligned reads in sam format. Note that DIAMOND has many output formats, so depending on your [choice](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options) with ` --diamond_output_format` you will receive the taxonomic information in a different format.
### MALT
@ -375,7 +377,7 @@ The main taxonomic profiling file from MetaPhlAn3 is the `*_profile.txt` file. T
</details>
By default, nf-core/taxprofiler is providing a column describing NCBI taxonomic ID as this is used in the taxpasta step. You can disable this column by activating the argument `--motus_remove_ncbi_ids`.
Normally `*_combined_reports.txt` is the most useful file for downstream analyses, but the per sample `.out` file can provide additional more specific information. By default, nf-core/taxprofiler is providing a column describing NCBI taxonomic ID as this is used in the taxpasta step. You can disable this column by activating the argument `--motus_remove_ncbi_ids`.
You will receive the relative abundance instead of read counts if you provide the argument `--motus_use_relative_abundance`.
### Krona