SOLiD SAGE: low percentage of reads mapped
Hello,
I was analyzing the SOLiD SAGE data of human sequence using SOLiD SAGE Analysis tool. I performed Mapping using 27 bp length with 1 mismatch. The reference was the complete set of human mRNA sequence from Refseq db. I then calculated % of reads that mapped to reference using the results file that gives the list of tags and their corresponding read files. I ran the analysis for 4 SAGE data and I got the following percentage:
SAGE A : 15 % apporx.; SAGE B 16% approx.; SAGE C 17% and SAGE D 20 %
What can be the reason for such low percentage of reads mapping to human mRNA reference? Is it a general result for most of the SOLiD SAGE experiments?
Thanks
PS: I'm sorry I'm posting the same thread again as I was not able to change the title of the old thread. Since it deals with SOLiD SAGE so I thought mentioning SOLiD SAGE in the title will help public to view this thread under SOLiD SAGE category.
