Hello Galaxy Experts
I have a query regarding "Get flanks" tool under "Operate on genomic intervals" to get the genomic sequences flanking all of the SNPs. I notice that it throws an error that it skips certain number of invalid lines. To let you know I have checked all the lines in the files from which I have fetched flanks from around SNPs and there seems to be no line without genomic coordinates or something which could be a source of error. My data has 770,000 SNPs. The tool has skipped 232217 lines which is a substantial number of SNPs.I want to identify these lines. Is there any way I can do it? On thinking on this issue I realise that there can insufficient coverage in this area, I definitely need to know what these lines are, and if possible get flanks for these SNPs.
I am in between of witting a full paper for which this information is very important. For these reasons I would appreciate early replies.