Hello Gonghong,
Yes, Novoalign is it's own beast (an excellent one at that) and is from Novocraft. So first run your reads through their aligner and then process your data with USeq. For chIP-seq you can probably get by with little loss in resolution using the xxx.sorted.gz alignments that came off the default Eland aligner that runs with the Illumina pipeline. Or barring those, use Bowtie for fast ungapped alignments.
-cheers, D
Yes, Novoalign is it's own beast (an excellent one at that) and is from Novocraft. So first run your reads through their aligner and then process your data with USeq. For chIP-seq you can probably get by with little loss in resolution using the xxx.sorted.gz alignments that came off the default Eland aligner that runs with the Illumina pipeline. Or barring those, use Bowtie for fast ungapped alignments.
-cheers, D
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