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This program reads three-letter mappings of bisulfite reads and computes local pairwise four-letter realignments using an advanced statistical alignment model.
Options
Input Ports
- SAM input file containing three-letter read alignments (must be sorted by query names). [bam,sam,sam.bgzf,sam.gz]
- A reference genome file. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
- Either one (single-end) or two (paired-end) read files. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
Views
- Bisar Std Output
- The text sent to standard out during the execution of Bisar.
- Bisar Error Output
- The text sent to standard error during the execution of Bisar. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)
Workflows
Links
- No links available
Developers
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