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
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...@@ -35,7 +35,7 @@ database computes these `.vidjil` files. ...@@ -35,7 +35,7 @@ database computes these `.vidjil` files.
Otherwise, such `.vidjil` files can be obtained: Otherwise, such `.vidjil` files can be obtained:
- from vidjil-algo (starting from - 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 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 - 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) 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, ...@@ -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. 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. 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: There can be several causes leading to bad ratios:
### Analysis or biological causes ### Analysis or biological causes
- The data actually contains other germline/locus that what was searched for - 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). (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. and contact us if you would like to analyze data from species that are not currently available.
- There are incomplete/exceptional recombinations - 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 - There are too many hypersomatic mutations
(usually Vidjil can process mutations until 10% mutation rate… above that threshold, some sequences may be lost). (usually Vidjil can process mutations until 10% mutation rate… above that threshold, some sequences may be lost).
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