Hello,
I trimmed the DNA fastq sequence (100bp) to 70bp and 50 bp because the quality score lowers after 50 and 70bp, in basis of the hyp that sequences with high quality would yield high snp calling, yet I got nothing (0) after trimmed while I got around 5000 SNPs with original sequences (100bp) aligned with the same MAQ with same parameters. Any suggestions? Thanks. john
I trimmed the DNA fastq sequence (100bp) to 70bp and 50 bp because the quality score lowers after 50 and 70bp, in basis of the hyp that sequences with high quality would yield high snp calling, yet I got nothing (0) after trimmed while I got around 5000 SNPs with original sequences (100bp) aligned with the same MAQ with same parameters. Any suggestions? Thanks. john