tag:blogger.com,1999:blog-36768584.post3399192051728268579..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Reanalysis Lays Bare MinION Review's Spectacular FlawsKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-36768584.post-38465185118918865952014-09-10T18:40:38.209-04:002014-09-10T18:40:38.209-04:00Sorry, wrong thought - error mode didn't matte...Sorry, wrong thought - error mode didn't matter, just error rate. If you picked too long a For the error rate, then few legitimate kmers will exist and you won't find your relationship.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-75050852512139429982014-09-10T11:37:40.579-04:002014-09-10T11:37:40.579-04:00The kmer analysis you describe is going to fail wi...The kmer analysis you describe is going to fail with high indel rates. <br /><br />What does this look like for raw PacBio CLR data? Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-67805890231454241552014-09-10T10:57:02.960-04:002014-09-10T10:57:02.960-04:00Hi Keith,
I did my own analysis and had trouble g...Hi Keith,<br /><br />I did my own analysis and had trouble getting anything meaningful. Maybe you can tell me where I am going wrong.<br /><br />I took all reads from Mikheyev's set and determined a k-mer distribution (k=12). If the data set is truly reflective of the genome, highly occurring kmers from that distribution should match the genome. I do not see that happening.<br /><br />I am doing the same analysis with Ecoli data now, and if that one works, then maybe the problem is with Mikheyev's data. <br /><br />Will get back to you. homolog.ushttp://homolog.usnoreply@blogger.com