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:

  1. Query/read sequence identifier
  2. Reference sequence identifier
  3. Percent identity of the alignment
  4. Not used
  5. Not used
  6. Not used
  7. Alignment start position on the query sequence
  8. Alignment stop position on the query sequence
  9. Alignment start position on the reference sequence
  10. Alignment stop position on the reference sequence
  11. Not used
  12. Not used
  13. Alignment score
  14. Query strand
  15. Reference sequence strand
  16. Query/read length
  17. 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
  18. Number of different alignments reported for this query sequence
  19. Not used
  20. 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.
  21. Reverse complemented unaligned query sequence from the beginning of the query, or ‘-‘ if the query aligns to the left edge
  22. Unaligned sequence at the end of the query, or ‘-‘
  23. Reference sequence identifier where the mate is aligned, if different from the identifier in column 2, otherwise ‘-‘
  24. 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
  25. Composite alignment score for all exons that belong to the fragment