From 084d3506b3efd4b6e66b7946864a3fed1a27c21a Mon Sep 17 00:00:00 2001 From: Mark Izraelson Date: Fri, 18 Aug 2023 15:23:06 +0300 Subject: [PATCH] fixed custom library tutorial example commands by adding species taxon-id --- docs/mixcr/guides/create-custom-library.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/mixcr/guides/create-custom-library.md b/docs/mixcr/guides/create-custom-library.md index 7fa99675..0b24d21f 100644 --- a/docs/mixcr/guides/create-custom-library.md +++ b/docs/mixcr/guides/create-custom-library.md @@ -33,11 +33,12 @@ mixcr buildLibrary --debug \ --d-genes-from-fasta d-genes.IGH.fasta \ # optional --c-genes-from-fasta c-genes.IGH.fasta \ # optional --chain IGH \ + --taxon-id 9741 \ --species phocoena \ phocoena-IGH.json.gz ``` -Here we precisely specified mandatory option `--v-gene-feature` to specify the exact [feature](../reference/ref-gene-features.md) for V genes (for other gene types MiXCR by default will use `JRegion`, `DRegion` and `CExon1` respectively). Here we also specified `--debug` option to check whether there are any problems with the resulting library (see [debugging section](#debugging)). +Here we precisely specified mandatory option `--v-gene-feature` to specify the exact [feature](../reference/ref-gene-features.md) for V genes (for other gene types MiXCR by default will use `JRegion`, `DRegion` and `CExon1` respectively). Here we also specified `--debug` option to check whether there are any problems with the resulting library (see [debugging section](#debugging)). Notice, that a correct NCBI species taxon-id is a mandatory parameter. To use this library with MiXCR one can just put it in the same directory from which you run MiXCR or under the library search path which can be found by running `mixcr -v`. Example usage: ``` @@ -118,6 +119,7 @@ mixcr buildLibrary \ --j-genes-from-species human \ --c-genes-from-species mouse \ --species humouse \ + --taxon-id 9606 \ humouse-IGH.json ``` @@ -130,9 +132,12 @@ mixcr buildLibrary \ --j-genes-from-species human \ --c-genes-from-species mouse \ --species humouse \ + --taxon-id 9606 \ humouse-IGH.json ``` +Notice that for these cases taxon-id can be either human, mouse or any custom number, because the species is set to a non-canonical `humouse`. + To use this library with MiXCR one can just put it in the same directory from which you run MiXCR or under the library search path which can be found by running `mixcr -v`. Example usage: ``` mixcr analyze generic-amplicon \