Hi all,
The annotation file provided by Illumina for RatRef Expression chip is poorly annotated. Since illumina stopped selling these chips they stopped updating their annotation as well. So I am REMOAT annotation and Ensembl annotion to get a better annotation when analysing my data. However, recently we obtained NGS data for our rat strains and we wanted to find out the probes targeted regions SNPs from our analysis. So pulled the probes coordination from REMOAT annotation and try to find if our snps genomic location are included within the range or the probe sequence and I got my results. But I realized that many illumina probe start and end sequence are not always 50bp from both REMOAT and Ensembl. So what I am trying to do now is to blast the probes sequence to rat genome reference and the output will be illumina ID probe sequence and a genomic coordination in an automated way whether using web based program or perl software ? Any suggestions ?