SOAP vs Bowtie output

[strob]

Hello all,

When I perform a SOAP and a Bowtie on my data (single reads) and map these reads against my reference sequence (using Sequencher), I get quite different results. When using SOAP, the reads align in blocks against the reference sequence; while for Bowtie, I get a much more equal distribution of the reads (see attachments). I used different parameters for both, but I always get the same results.

Do you experience the same?
What could be the cause of this (bioinformatics or non-bioinformatics)?

Any help more than welcome,

Thanks,

Steven

[strob]

Nobody using SOAP neither Bowtie...??

[strob]

Can maybe somebody say how their results look like? Blocks or a continuous stretch of reads?

Many thanks

[Chipper]

Perhaps nobody uses Sequencer. Does the blocks mean part of the reference is not covered by SOAP alignments? What settings did you use, perhaps bowtie is set to report random hits for reads with multiple mappings while SOAP will only give you unique mappings?