Hi,
I had a RNA-Seq data in pig muscle tissue and assembled my sequence using
trinity, then I want to see how many sequence was overlapped with pig gene
intron, I first downloaded the position of each pig gene from NCBI based on the
sus genome 10.2 and BLAT my sequence vs sus genome 10.2. You said that when a
single mRNA aligned in multiple places, the alignment having the highest base
identity was found. Only alignments having a base identity level within 0.5% of
the best and at least 96% base identity with the genomic sequence were kept.
However, some sequence have mutipostion that don't have a bese identity level
within 0.5% but have 95% identity and 90% of their length, so should I take all
the mutiposition that just meet 95% identity and 90% of their length or the
mutiposion that meet your criterion to aganist the position of pig gene from
NCBI? Thanks a lot!
Best Wishes!
weimin zhao
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