Hi darked89,
Yes, you can use just the unmapped reads. I have been doing this for a while, and the results of using unmapped reads and the full dataset are virtually the same. As far as I know, HMMSplicer doesnt rely on exon islands so the unspliced reads dont really contribute to the search. Please correct me if I am wrong.
I suggest you to pool all the unmapped reads from multiple lanes as a single file.
Yes, you can use just the unmapped reads. I have been doing this for a while, and the results of using unmapped reads and the full dataset are virtually the same. As far as I know, HMMSplicer doesnt rely on exon islands so the unspliced reads dont really contribute to the search. Please correct me if I am wrong.
I suggest you to pool all the unmapped reads from multiple lanes as a single file.
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