I had a general query with short fixed length reads. Though I intend it for Solexa data only, it might be directly applicable to solid as well
For analysis after obtaining the set of reads, do people prefer taking a unique non redundant set of reads, before doing analysis like snp discovery, chip-seq, etc? Are the exactly same reads any information?
for de novo assembly, velvet behaves slightly different with a unique set of reads, than with some of the reads repeated.
For analysis after obtaining the set of reads, do people prefer taking a unique non redundant set of reads, before doing analysis like snp discovery, chip-seq, etc? Are the exactly same reads any information?
for de novo assembly, velvet behaves slightly different with a unique set of reads, than with some of the reads repeated.
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