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.
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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
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