RNA-seq reads BLAT

baohua100

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RNA-seq reads BLAT

08-23-2009, 10:30 AM

After align the reads to genome and junction sequences, I align the lefted reads to genome using BLAT. The read length: some 36bp and some 50bp.

BLAT outputs the PSL files. How can I use this file to confirm the four boundaries (start and end position of first and second exon where the read mapped) ?

like one read (36bp) maping on

chr 1 15677-15684 19887-19914

15685-19886 is a intron
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