Commit 7f1a9331 authored by Mathieu Giraud's avatar Mathieu Giraud

Apply 2 suggestion(s) to 1 file(s)

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......@@ -697,14 +697,7 @@ Presets
It is possible to extract all reads with or without detected recombinations,
possibly to give them to other software.
The recommanded way is to use the `--filter-reads` preset, that launches Vidjil-algo without clone clustering and analysis,
while outputing a `out/basename.detected.vdj.fa` file. This file contains reads /that may have V(D)J recombinations/,
evaluated with a very permissive threshold.
This preset is very useful for whole RNA-Seq or capture datasets that contain few reads with V(D)J recombinations
Internally, running Vidjil-algo with `-U` gives such a file `out/basename.detected.vdj.fa`, with all detected reads.
This detection only relies on the ultra-fast first pass analysis (`-c detect`), based on k-mer heuristics.
Other options are available to get the non analyzed reads:
- `-U` gives a file `out/basename.detected.vdj.fa` with all reads having a detected V(D)J recombination
- `-u` gives a set of files `out/basename.UNSEG_*`, with not detected reads gathered by cause.
It outputs only reads sharing significantly sequences with V/J germline genes or with some ambiguity:
......@@ -718,7 +711,10 @@ However, they are very useful in some situations, especially to understand
why some dataset gives low detection rate.
For example `-uu -X 1000` splits the not detected reads from the 1000 first reads.
When processing large datasets, such as RNA-Seq or capture, one may want to pre-filter read by keeping only the ones that potentially harbour a V(D)J recombination.
In such a case, the recommanded option is to use the `--filter-reads` preset, that launches Vidjil-algo without clone clustering and analysis,
while outputing a `out/basename.detected.vdj.fa` file. This file contains reads /that may have V(D)J recombinations/, evaluated with a very permissive threshold.
The resulting file is usually much smaller on such datasets and can then be transferred or analysed in-depth more easily.
## AIRR .tsv output
Since version 2018.10, vidjil-algo supports the [AIRR format](http://docs.airr-community.org/en/latest/datarep/rearrangements.html#fields).
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