Commit f71bffa6 authored by Mikaël Salson's avatar Mikaël Salson

user.md: Update algo.org locus.org links

parent e96e6d5e
Pipeline #58277 failed with stages
in 45 seconds
......@@ -35,7 +35,7 @@ database computes these `.vidjil` files.
Otherwise, such `.vidjil` files can be obtained:
- from vidjil-algo (starting from
`.fasta`, `.fastq` or `.gz` files, see [algo.org](http://git.vidjil.org/blob/master/doc/algo.org)).
`.fasta`, `.fastq` or `.gz` files, see [vidjil-algo documentation](http://www.vidjil.org/doc/vidjil-algo/)).
To gather several `.vidjil` files, you have to use the [fuse.py](http://git.vidjil.org/blob/master/tools/fuse.py) script
- or by any other V(D)J analysis pipelines able to output files
respecting the `.vidjil` [file format](./format-analysis.org) (contact us if you are interested)
......@@ -429,18 +429,18 @@ With DNA-Seq sequencing with specific V(D)J primers,
ratios above 90% usually mean very good results. Smaller ratios, especially under 60%, often mean that something went wrong.
On the other side, capture with many probes or RNA-Seq strategies usually lead to datasets with less than 0.1% V(D)J recombinations.
The “info“ button further detail the causes of non-analysis (for vijdil-algo, `UNSEG`, see detail on [algo.org](http://git.vidjil.org/blob/master/doc/algo.org)).
The “info“ button further detail the causes of non-analysis (for vijdil-algo, `UNSEG`, see detail on [vidjil-algo documentation](http://www.vidjil.org/doc/vidjil-algo/#unsegmentation-causes)).
There can be several causes leading to bad ratios:
### Analysis or biological causes
- The data actually contains other germline/locus that what was searched for
(solution: relauch the processing, or ask that we relaunch it, with the correct germline sequences).
See [locus.org](http://git.vidjil.org/blob/master/doc/locus.org) for information on the analyzable human locus with vidjil-algo,
See [locus documentation](http://www.vidjil.org/doc/locus/) for information on the analyzable human locus with vidjil-algo,
and contact us if you would like to analyze data from species that are not currently available.
- There are incomplete/exceptional recombinations
(Vidjil can process some of them, config `multi+inc`, see [locus.org](http://git.vidjil.org/blob/master/doc/locus.org) for details)
(Vidjil can process some of them, config `multi+inc`, see [locus documentation](http://www.vidjil.org/doc/locus/) for details)
- There are too many hypersomatic mutations
(usually Vidjil can process mutations until 10% mutation rate… above that threshold, some sequences may be lost).
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment