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dbolotin committed Aug 13, 2015
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9 changes: 9 additions & 0 deletions doc/example_output.rst
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+---------------+------------------+-------+------------------------------------------+-----------------+-------------------+--------------------------+-----------------+-------+
| Clone count | Clone fraction | ... | V hits | J hits | ... | N. seq. CDR3 | AA. seq. CDR3 | ... |
+===============+==================+=======+==========================================+=================+===================+==========================+=================+=======+
| 4369 | 2.9E-3 | ... | IGHV4-39*00(1388) | IGHJ6*00(131) | ... | TGTGTGAG...GACGTCTGG | CVRHKPMVQGGVDVW | ... |
+---------------+------------------+-------+------------------------------------------+-----------------+-------------------+--------------------------+-----------------+-------+
| 3477 | 2.3E-3 | ... | IGHV4-34*00(1944) | IGHJ4*00(153) | ... | TGTGCGAT...ATGACTTCTGG | CAIWDVGLRHDFW | ... |
+---------------+------------------+-------+------------------------------------------+-----------------+-------------------+--------------------------+-----------------+-------+
| ... | ... | ... | ... | ... | ... | ... | ... | ... |
+---------------+------------------+-------+------------------------------------------+-----------------+-------------------+--------------------------+-----------------+-------+
118 changes: 49 additions & 69 deletions doc/quickstart.rst
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Expand Up @@ -50,8 +50,8 @@ The value of only one parameter is changed from its default in this snippet (``-

The file produced (``clone.txt``) will contain a tab-delimited table with information about all clonotypes assembled by CDR3 sequence (clone abundance, CDR3 sequence, V, D, J genes, etc.). For full length analysis and other useful features see examples below.

E2. Analysis of data obtained using 5'RACE-based amplification protocols
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Analysis of data obtained using 5'RACE-based amplification protocols
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Consider MiXCR workflow in more detail on analysis of paired-end
sequenced cDNA library of IGH gene prepared using 5'RACE-based protocol
Expand All @@ -61,87 +61,67 @@ sequenced cDNA library of IGH gene prepared using 5'RACE-based protocol
1. `Align <#align>`__ raw sequences to reference sequences of segments
(V, D, J) of IGH gene:

::
.. code-block:: console
> mixcr align --loci IGH -OvParameters.geneFeatureToAlign=VTranscript --report alignmentReport.log input_R1.fastq input_R2.fastq alignments.vdjca
> mixcr align --loci IGH -OvParameters.geneFeatureToAlign=VTranscript --report alignmentReport.log input_R1.fastq input_R2.fastq alignments.vdjca
Here we specified non-default value for gene feature used to align V
genes (``-OvParameters.geneFeatureToAlign=VTranscript``) in order to
utilize information from both reads, more specifically to let MiXCR
align V gene's 5'UTRS and parts of coding sequence on 5'-end with
sequence from read opposite to CDR3. MiXCR can also produce report
file (specified by optional parameter ``--report``) containing run
statistics which looks like this:
Here we specified non-default value for gene feature used to align V genes (``-OvParameters.geneFeatureToAlign=VTranscript``) in order to utilize information from both reads, more specifically to let MiXCR align V gene's 5'UTRS and parts of coding sequence on 5'-end with sequence from read opposite to CDR3. MiXCR can also produce report file (specified by optional parameter ``--report``) containing run statistics which looks like this:

::
::

Analysis Date: Mon Aug 25 15:22:39 MSK 2014
Input file(s): input_r1.fastq,input_r2.fastq
Output file: alignments.vdjca
Command line arguments: align --loci IGH --report alignmentReport.log input_r1.fastq input_r2.fastq alignments.vdjca
Total sequencing reads: 323248
Successfully aligned reads: 210360
Successfully aligned, percent: 65.08%
Alignment failed because of absence of V hits: 4.26%
Alignment failed because of absence of J hits: 30.19%
Alignment failed because of low total score: 0.48%
Analysis Date: Mon Aug 25 15:22:39 MSK 2014
Input file(s): input_r1.fastq,input_r2.fastq
Output file: alignments.vdjca
Command line arguments: align --loci IGH --report alignmentReport.log input_r1.fastq input_r2.fastq alignments.vdjca
Total sequencing reads: 323248
Successfully aligned reads: 210360
Successfully aligned, percent: 65.08%
Alignment failed because of absence of V hits: 4.26%
Alignment failed because of absence of J hits: 30.19%
Alignment failed because of low total score: 0.48%

One can convert binary output produced by ``align``
(``output.vdjca``) to a human-readable text file using
`exportAlignments <#export>`__ command.
One can convert binary output produced by ``align`` (``output.vdjca``) to a human-readable text file using `exportAlignments <#export>`__ command.

- `Assemble <#assemble>`__ clonotypes:
2. `Assemble <#assemble>`__ clonotypes:

::
.. code-block:: console
> mixcr assemble --report assembleReport.log alignments.vdjca clones.clns
> mixcr assemble --report assembleReport.log alignments.vdjca clones.clns
This will build clonotypes and additionally correct PCR and
sequencing errors. By default, clonotypes will be assembled by CDR3
sequences; one can specify another gene region by passing additional
command line arguments (see `assemble <#assemble>`__ documentation).
The optional report ``assembleReport.log`` will look like:
This will build clonotypes and additionally correct PCR and
sequencing errors. By default, clonotypes will be assembled by CDR3
sequences; one can specify another gene region by passing additional
command line arguments (see `assemble <#assemble>`__ documentation).
The optional report ``assembleReport.log`` will look like:

::
::

Analysis Date: Mon Aug 25 15:29:51 MSK 2014
Input file(s): alignments.vdjca
Output file: clones.clns
Command line arguments: assemble --report assembleReport.log alignments.vdjca clones.clns
Final clonotype count: 11195
Total reads used in clonotypes: 171029
Reads used, percent of total: 52.89%
Reads used as core, percent of used: 92.04%
Mapped low quality reads, percent of used: 7.96%
Reads clustered in PCR error correction, percent of used: 0.04%
Clonotypes eliminated by PCR error correction: 72
Percent of reads dropped due to the lack of clonal sequence: 2.34%
Percent of reads dropped due to low quality: 3.96%
Percent of reads dropped due to failed mapping: 5.87%

- `Export <#export>`__ binary file with a list of clones
(``clones.clns``) to a human-readable text file:
Analysis Date: Mon Aug 25 15:29:51 MSK 2014
Input file(s): alignments.vdjca
Output file: clones.clns
Command line arguments: assemble --report assembleReport.log alignments.vdjca clones.clns
Final clonotype count: 11195
Total reads used in clonotypes: 171029
Reads used, percent of total: 52.89%
Reads used as core, percent of used: 92.04%
Mapped low quality reads, percent of used: 7.96%
Reads clustered in PCR error correction, percent of used: 0.04%
Clonotypes eliminated by PCR error correction: 72
Percent of reads dropped due to the lack of clonal sequence: 2.34%
Percent of reads dropped due to low quality: 3.96%
Percent of reads dropped due to failed mapping: 5.87%

::
3. `Export <#export>`__ binary file with a list of clones (``clones.clns``) to a human-readable text file:

> mixcr exportClones clones.clns clones.txt
.. code-block:: console
> mixcr exportClones clones.clns clones.txt
This will export information about clones with default set of fields, e.g.:

.. include:: example_output.rst

This will export information about clones with default set of fields,
e.g.:

+---------------+------------------+-------+------------------------------------------+----------+--------------------------+-------------------+-----------------+-------+
| Clone count | Clone fraction | ... | V hits | J hits | ... | N. seq. CDR3 | AA. seq. CDR3 | ... |
+===============+==================+=======+==========================================+==========+==========================+===================+=================+=======+
| 4369 | 2.9E-3 | ... | IGHV4-39\ *00(1388) \| IGHJ6*\ 00(131) | ... | TGTGTGAG...GACGTCTGG | CVRHKPMVQGGVDVW | ... |
+---------------+------------------+-------+------------------------------------------+----------+--------------------------+-------------------+-----------------+-------+
| 3477 | 2.3E-3 | ... | IGHV4-34\ *00(1944) \| IGHJ4*\ 00(153) | ... | TGTGCGAT...ATGACTTCTGG | CAIWDVGLRHDFW | ... |
+---------------+------------------+-------+------------------------------------------+----------+--------------------------+-------------------+-----------------+-------+
| ... | ... | ... | ... | ... | ... | ... | ... | ... |
+---------------+------------------+-------+------------------------------------------+----------+--------------------------+-------------------+-----------------+-------+

where dots denote rows not shown here (for compactness). For the full
list of available export options see `export <#export>`__
documentation.
where dots denote rows not shown here (for compactness). For the full list of available export options see `export <#export>`__ documentation.

Each of the above steps can be customized in order to adapt the analysis
pipeline for a specific research task (see below).
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