ContextMap 2.0
Warning
Make sure to put the file jre-8u241-linux-i586.tar.gz in the same folder as the ContextMap Dockerfile (src/contextmap2/).nYou can get the file here: https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html
Indexing
Note
Indexing might take some time but only has to be run once per fasta file. Make sure to reuse already computed indices if possible.
DICAST will check if $indexdir/$indexname exists. If there is no index it will be automatically built. If you want to rebuild the index anyway set $recompute_index=true in scripts/mapping_config.sh.
If you want to use your own precomputed index file copy it to index/contextmap-index/ and make sure the index is complete and named appropriately and according to the parameters set in the config files.
We recommend including the name of the fasta file in the index name to avoid overwriting. Per default this is already the case and no parameter changes are needed.
Parameters
These are the default parameters set in the src/contextmap/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the ContextMap 2.0 manual.
- -reads
Comma separated list of file paths to reads in fastq format. One pair of fastq files for paired-end mapping
-reads *yourFastqFile1_*1.fastq,*yourFastqFile1_*2.fastq- -aligner_name
Used aligner (index tool). We use bowtie2.
-aligner_name bowtie2- -aligner_bin
Path to the used aligner. If you use our docker you will not have to wolly about it.
-aligner_bin /home/biodocker/bin/bowtie2- -indexer_bin
Path to the indexing tool of the aligner.
-indexer_bin /home/biodocker/bin/bowtie2-build- -indices
Comma separated list to your index files base names.
-indices *IndexChromosome1*,*IndexChromosomes2*,*IndexChromosome3*, . . .- -genome
Directory path with chromosome-wise fasta files.
-genome $bowtie_fastadir