From 362193f071fdb802a26418bb8eb9cc5477a5f6d2 Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Thu, 11 Jul 2019 16:59:53 +0200 Subject: [PATCH] doc/vidjil-format.md: corrections Thanks to the discussion with Patrice and @espyr. --- doc/vidjil-format.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/doc/vidjil-format.md b/doc/vidjil-format.md index 7a9a2f59a..17d9d2e31 100644 --- a/doc/vidjil-format.md +++ b/doc/vidjil-format.md @@ -37,7 +37,9 @@ This is an almost minimal `.vidjil` file, describing clones in one sample. The `seg` element is optional: clones without `seg` elements will be shown on the grid with '?/?'. The `_average_read_length` is also optional, but allows to plot GENSCAN-like plots more precisely than getting only the length of the sequence. All other elements are required. The `reads.germlines` list can have only one element the case of data on a unique locus. -There is here one clone on the `TRG` locus with a designation `TRGV5*01 5/CC/0 TRGJ1*02`. +There is here one clone on the `TRG` locus with a designation (`name`) `TRGV5*01 5/CC/0 TRGJ1*02`. +Note that this `name` is just used to name the clone. +The actual values used for X- and Y- axis in the V/J grid plot are `seg.5.name` and `seg.3.name` fields. Note that other elements could be added by some program (such as `tag`, to identify some clones, or `clusters`, to further cluster some clones, see below). @@ -65,6 +67,7 @@ or `clusters`, to further cluster some clones, see below). "clones": [ { "id": "clone-001", + "name": "TRGV5*01 5/CC/0 TRGJ1*02", "sequence": "CTCATACACCCAGGAGGTGGAGCTGGATATTGATACTACGAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGCCTTATTATAAGAAACTCTTTGGCAGTGGAAC", "reads" : [ 243241 ], "_average_read_length": [ 119.3 ], @@ -85,7 +88,7 @@ or `clusters`, to further cluster some clones, see below). ## `.vidjil` file – several related samples This a `.vidjil` file obtained by merging with `fuse.py` two `.vidjil` files corresponding to two samples. -Clones that have a same `id` are gathered (see 'What is a clone?', above). +Clones that are from different files but that have a same `id` are gathered (see 'What is a clone?', above). It is the responsibility of the program generating the initial `.vidjil` files to choose these `id` to do a correct gathering. -- GitLab