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
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