sc_read_kallisto_wrapper https://github.com/vibbits/sc_read_kallisto_wrapper Copyright (c) BITS VIB 2017
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or any later version.
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Full license text can be found in LICENSE.txt
The sc_read_kallisto_wrapper takes as input a BCL file generated by an Illumina sequencer run on a 10XGENOMICS Chromium single cell 3' RNA-seq library, extracts the reads, maps them to a transcriptome using kallisto and formats the equivalence class counts as input for Seurat.
It is necessary to install the latest versions of CellRanger, bcl2fastq and kallisto.
The script sc_read_kallisto_wrapper.pl must, before it can be used, be modified. There is a block of code "These must be adapted appropriately". The shebang "#!/usr/bin/perl" at the top might have to be modified as well.
Type ./sc_read_kallisto_wrapper.pl -h to obtain information about how to format the command line. There is a stand-alone HTML file sc_read_kallisto_wrapper.html with more information about what the wrapper does. You can find the same information in the wiki
What if I have no BCL file ?
If you have no access to the BCL file because the lab sent you directly the fastQ files, you can use instead sc_read_kallisto_simplewrapper.pl. Make sure the fastQ files respect the naming convention. The files must have names
test_sample_S1_L001_R1_001.fastq.gz
where
- test_sample is the sample name
- S1 is S followed by a sample number
- R1 is R or I followed by a number