Dear list,
I am not sure if this question belongs to the bioinformatics section, but it is indeed a basic question. In the case of a tumor experiment, one could expect large rearrangements, big enough to delete several introns and exons from a gene. Is it possible to detect such large rearrangements using 35 base-long Solexa reads? How big indels could I detect? I guess if the experiment was a pair-end one, that way you could probably detect heterozygous indels. How about homozygous ones? Is it possible to detect this kind of indels by visualizing alignment patterns with, for example, maqview looking for alignment gaps?
Thanks for your help
Dave
I am not sure if this question belongs to the bioinformatics section, but it is indeed a basic question. In the case of a tumor experiment, one could expect large rearrangements, big enough to delete several introns and exons from a gene. Is it possible to detect such large rearrangements using 35 base-long Solexa reads? How big indels could I detect? I guess if the experiment was a pair-end one, that way you could probably detect heterozygous indels. How about homozygous ones? Is it possible to detect this kind of indels by visualizing alignment patterns with, for example, maqview looking for alignment gaps?
Thanks for your help
Dave
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