In my research project I am undertaking I have mined about 200,000 SNPs. I have extracted DNA sequences upstream and downstream out of them but I am unable to align them to the right places. I am writing you a quick steps i followed. After extracting SNPs in the VCF file I have used get flanks to obtain the flanks of the SNP position, this step skipped several lines inspite of data input in the correct format. Then i used extract genomic DNA out of each flank both upstream and downstream.But the output which I obtained are in interval format with genomic sequences on both sides, but still there are some lines skipped. Now from whatever results I get I want to align sequences to go with the correct SNPs. Can anybody please suggest me how can this be done in galaxy?
A very big thank you in advance. D