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hi all!
Recently I met with a very tricky problem:
In order to ensure that the reads I mapped with bwa all have single hit on genome, I extracted all reads around snps called and re-map them with blat.
I found that if I only map a small section of paired-end reads(943×2) with blat, I can get a psl file with 943 lines in it; but if I map all reads(208149300×2) to genome which include the 943×2 reads, I only got 699 lines came from the 943×2 reads in final psl file.
Why is that? Is is possible that the number of queries can affect the result of blat?
Thanks a lot!
Recently I met with a very tricky problem:
In order to ensure that the reads I mapped with bwa all have single hit on genome, I extracted all reads around snps called and re-map them with blat.
I found that if I only map a small section of paired-end reads(943×2) with blat, I can get a psl file with 943 lines in it; but if I map all reads(208149300×2) to genome which include the 943×2 reads, I only got 699 lines came from the 943×2 reads in final psl file.
Why is that? Is is possible that the number of queries can affect the result of blat?
Thanks a lot!