Output
By default, results are provided to the standard output in the SAM format.
Use -out <filename> option to redirect output to a file.
Use -outfmt option to specify the output format:
-outfmt sam : SAM format (default)
-outfmt tabular : exports a simple tab delimited format defined below.
The output can be also compressed, using the -gzo flag:
magicblast -query reads.fa -db genome -out output.gz -gzo
Unaligned reads
By default Magic-BLAST reports unaligned reads, with unmapped bit (4) set in SAM flags or ‘*’ in the second column of the tabular output. If you do not want unmapped reads reported, use -no_unaligned option:
magicblast -query reads -db reference -no_unaligned
Tabular output format
The tabular output format shows one alignment per line with these tab delimited fields:
- Query/read sequence identifier
- Reference sequence identifier
- Percent identity of the alignment
- Not used
- Not used
- Not used
- Alignment start position on the query sequence
- Alignment stop position on the query sequence
- Alignment start position on the reference sequence
- Alignment stop position on the reference sequence
- Not used
- Not used
- Alignment score
- Query strand
- Reference sequence strand
- Query/read length
- Alignment as extended BTOP string
This is the same BTOP string as in BLAST tabular output with a
few extensions:
- a number represents this many matches,
- two bases represent a mismatch and show query and reference base,
- base and gap or gap and base, show a gap in query or reference,
- ^<number>^ represents an intron of this number of bases,
- _<number>_ represents an insertion (gap in reference) of this number of bases,
- %<number>% represents a deletion (gap in read) of this number of bases,
- (<number>) shows number of query bases that are shared between two parts of a spliced alignment; used when proper splice sites were not found
- Number of different alignments reported for this query sequence
- Not used
- Compartment - a unique identifier for all alignments that belong to a single fragment. These can be two alignments for a pair of reads or alignments to exons that were not spliced.
- Reverse complemented unaligned query sequence from the beginning of the query, or ‘-‘ if the query aligns to the left edge
- Unaligned sequence at the end of the query, or ‘-‘
- Reference sequence identifier where the mate is aligned, if different from the identifier in column 2, otherwise ‘-‘
- Alignment start position on the reference sequence for the mate, or ‘-‘ if no alignment for the mate was found; a negative number denotes a divergent pair
- Composite alignment score for all exons that belong to the fragment