Commit f8b13f31 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: --filter-reads, and rework help on --out-detected

closes #4681
parent d90203ba
Pipeline #214659 passed with stages
in 35 minutes and 53 seconds
......@@ -689,17 +689,22 @@ Detailed output per read (generally not recommended, large files, but may be use
-uuu output undetected reads, all reads, including a .undetected.vdj.fa file (use only for debug)
--out-reads output all reads by clones (clone.fa-*), to be used only on small datasets
-K, --out-affects output detailed k-mer affectation for each read (in .affects file) (use only for debug, for example -KX 100)
Presets
--filter-reads filter possibly huge datasets, with a permissive threshold, to extract reads that may have V(D)J recombinations
(equivalent to -c detect --out-detected --e-value 1e6 -2)
```
It is possible to extract all reads with or without detected recombinations,
possibly to give them to other software.
Runing Vidjil-algo with `-U` gives a file `out/basename.detected.vdj.fa`, with all detected reads.
On datasets generated with rather specific V(D)J primers, this is generally not recommended, as it may generate a large file.
However, the `-U` option is very useful for whole RNA-Seq or capture datasets that contain few reads with V(D)J recombinations.
Moreover `-U` only uses the ultra-fast first passs analysis, based on k-mer heuristics.
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
Similarly, options are available to get the non analyzed reads:
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 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:
......@@ -708,7 +713,7 @@ Similarly, options are available to get the non analyzed reads:
- `-uu` gives the same set of files, including **all** not detected reads (including `UNSEG too short` and `UNSEG too few V/J`),
and `-uuu` further outputs all these reads in a file `out/basename.undetected.vdj.fa`.
Again, as these options may generate large files, they are generally not recommended.
As these options may generate large files, they are generally not recommended.
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.
......
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