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i mapped my reads by tophat.and i don't think the junction reads generated by tophat are reliable. so when i do SNP calling, i don't want the SNPs near to junction? is there any practical way to handle this?
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Call your SNPs, get your junction locations, and then filter your SNPs. -
thank you very much.it is better than "filter first, call SNP then" strategy. another question: if some reads has more mismatches on the end, but it's very difficult for me to find and clip them, because i don't know which read has this problem. is there any tool or SNP-calling model to handle this?Originally posted by JohnK@Genome_Quest View PostLast edited by chenjy; 07-30-2011, 02:56 AM.Comment
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