non-overlapping reads in isotigs (screenshot)

[simoblimo]

Hi,

Im new to the GS assembler and have a question regarding isotigs and non-overlapping reads in the alignment result screen of the GS-software.

Please see the screen shot picture in the attached .zip file. It seems to me that the assembly have included many reads (in yellow) which do not overlap at all with any of the reads that are similar to the reference sequence. This puzzles7worries me, but perhaps I have misunderstood something?

Anyone have an idea?

Ciao!
Simen

[flxlex]

My guess is the reads at the top (left) are in a different contig than the ones below (the yellow ones). Isotigs are concatenated contigs, and in the ace file only the parts of the reads present in the contigs in question are included. Perhaps if you were able to open the ace file in consed, you might see the unused parts of reads again...

[Jeremy]

Is this from gsMapper? Can you please give us the details of what you have done?

Your mention of reference sequence makes me think it is gsMapper, and isotigs suggests you have done RNA-Seq.