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Fix for wrong hyphen symbol in quickstart ( dash (U+2013) -> hyphen-m…

…inus (U+002D) )
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dbolotin committed Mar 27, 2017
1 parent e5a386c commit 8d281597d7dfcd0683657dfb2d2bd54945fe24d4
Showing with 6 additions and 6 deletions.
  1. +6 −6 doc/quickstart.rst
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@@ -174,11 +174,11 @@ For the full length cDNA-based immunoglobulin repertoire analysis we generally r
::
> mixcr align -p kaligner2 s hsa -r alignmentReport.txt -OreadsLayout=Collinear \
> mixcr align -p kaligner2 -s hsa -r alignmentReport.txt -OreadsLayout=Collinear \
-OvParameters.geneFeatureToAlign=VTranscript read_R1.fastq.gz read_R2.fastq.gz \
alignments.vdjca
Option ``-s`` allows to specify species (e.g. homo sapiens - ``hsa``, mus musculus - ``mmu``). Parameter ``OreadsLayout`` allow us to set paired-end reads orientation (``Collinear``, ``Opposite``, ``Unknown``). Note, that after MiGEC analysis paired-end read pairs are in ``Collinear`` orientation.
Option ``-s`` allows to specify species (e.g. homo sapiens - ``hsa``, mus musculus - ``mmu``). Parameter ``-OreadsLayout`` allow us to set paired-end reads orientation (``Collinear``, ``Opposite``, ``Unknown``). Note, that after MiGEC analysis paired-end read pairs are in ``Collinear`` orientation.
Instead of KAligner2, default MiXCR aligner can be used as well, but it may miss immunoglobulin subvariants that contain several nucleotide-lengths indels within the V gene segment.
@@ -187,13 +187,13 @@ For the full length cDNA-based immunoglobulin repertoire analysis we generally r
::
> mixcr assemble -p default_affine -r assembleReport.txt -OassemblingFeatures=VDJRegion \
OseparateByC=true -OqualityAggregationType=Average \
-OseparateByC=true -OqualityAggregationType=Average \
-OclusteringFilter.specificMutationProbability=1E-5 -OmaxBadPointsPercent=0 \
alignments.vdjca clones.clns
``default_affine`` parameter is specifically required for the data aligned using KAligner2 (use this option only if ``-p kaligner2`` was used on the alignemnt step)
``OseparateByC=true`` separates clones with different antibody isotype.
``-OseparateByC=true`` separates clones with different antibody isotype.
Set ``-OcloneClusteringParameters=null`` parameter to switch off the frequency-based correction of PCR errors.
@@ -205,9 +205,9 @@ For the full length cDNA-based immunoglobulin repertoire analysis we generally r
::
> mixcr exportClones c IGH -o -t clones.clns clones.txt
> mixcr exportClones -c IGH -o -t clones.clns clones.txt
where options ``-o`` and ``-t`` filter off the out-of-frame and stop codon containing clonotypes, respectively, and ``c`` indicates which chain will be extracted (e.g. ``IGH``, ``IGL``).
where options ``-o`` and ``-t`` filter off the out-of-frame and stop codon containing clonotypes, respectively, and ``-c`` indicates which chain will be extracted (e.g. ``IGH``, ``IGL``).
.. _ref-exampleRnaSeq:

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