Our results based on read quality, homology, ORF, GO based functional analysis, full length cDNA, and comparative genomic analysis suggest that we have successfully found genes in camel matched to known coding sequences in other organisms and novel gene sequences with a protein coding capacity.
From among the 2507 putative SNP discovered in silico, 1369 were chosen to be experimentally validated based on read quality and number of reads with rare allele.
TopHat removes a small number of reads based on read quality and then maps the reads to a provided reference genome sequence.
Filtering based on read quality is not sufficient per se, which caused us to make an assessment of the reliability of a read based on its abundance relative to the abundance of any other reads with highly related sequences.
In a sequencing experiment of genomic DNA, sequencing error can largely be accounted for by filtering based on read quality and/or the imposition of a suitable lower limit in read depth.
