Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD

Similar Threads
Thread Thread Starter Forum Replies Last Post
GAII low number of mapped reads aligenie Bioinformatics 3 06-21-2011 11:55 PM
expected percentage of mapped reads in chip-seq experiment andreiafonseca General 16 03-25-2011 05:14 AM
Percentage of mapped reads ? zack80.liu Bioinformatics 6 03-01-2011 09:08 AM
SOLiD SAGE reads direction and orientation invermay SOLiD 0 02-14-2011 06:17 PM
low percentage of reads mapped rahilsethi SOLiD 3 09-13-2010 06:01 AM

Thread Tools
Old 09-09-2010, 11:04 AM   #1
Location: Pittsburgh, PA

Join Date: May 2010
Posts: 22
Post SOLiD SAGE: low percentage of reads mapped


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?


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.
rahilsethi is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:37 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO