Align bisulfite converted reads to a reference genome using bowtie2
gpatterns.bissli2(r1_fastq, out_bam, genome_seq, bissli2_idx, r2_fastq = NULL,
bissli2_bin = .gpatterns.bissli2_bin, bowtie2 = "bowtie2",
samtools = "samtools", maxins = 1000, threads = 10,
genome_type = "ct", tmp_dir = NULL, bissli2_params = "")
Arguments
- r1_fastq
- a vector of FASTQ files to align (read1)
- out_bam
- bam output file with aligned reads
- genome_seq
- A directory holding the reference genome, one FASTA file per
chromosome
- bissli2_idx
- The basename of the index to be searched. The index is created using
gpatterns.bissli2_build
- r2_fastq
- a vector of FASTQ files to align (read2)
- bissli2_bin
- path for bissli2-align
- bowtie2
- path for bowtie2
- samtools
- path for samtools
- maxins
- maximum fragment length (bowtie2 maxins argument)
- threads
- number of threads to use
- genome_type
- ct/ga/ct_ga. if 'ct' - Assume that the reads to be aligned underwent C->T conversion. If
paired-end reads are aligned, then assume read 1 underwent C->T
conversion while read 2 underwent G->A conversion. The --ct and --ga
options are mutually exclusive. if 'ga' - Assume that the reads to be aligned underwent G->A conversion. If
paired-end reads are aligned, then assume read 1 underwent G->A
conversion while read 2 underwent C->T conversion.
if 'ct_ga' reads would be aligned to both C->T and G->A, and the best match would
be chosen.
- tmp_dir
- Directory for storing temporary files
- bissli2_params
- additional parameters to bissli2/bowtie2