Bfast alignment

[madhu]

I used Bfast to align my Chip-Seq data. Unfortunately the percentage of reads got aligned is very less.
I used the default parameters to run 'matches' and 'local align'

This is the log information:

Performing alignment...
Reads processed: 12000000
Alignment complete.
Performed 859254 local alignments.
Outputted alignments for 112106 reads.
Outputted 11887894 reads for which there were no alignments.
Outputting complete.
*********************************************************

Please let me know.. why I get such a low percentage of aligned read in Bfast?

Also i used Bowtie to align the same data, I got very different result:

# reads processed: 12000000
# reads with at least one reported alignment: 11220913 (93.51%)
# reads that failed to align: 779087 (6.49%)
Reported 11220913 alignments to 1 output stream(s)

Thanks,
Madhu

[nilshomer]

Is this SOLiD or Illumina data? Can you show us the commands you used, as well as the BFAST version #?

[madhu]

This is Illumina data.
I used ./bfast localalign -f ../../genomes/mm9_genome.fa -m $list\_matches.bmf -u -t > $list\_bfast.aligned.file.baf

[nilshomer]

Remove the "-u" option.