Hi list members, Is there an effective way for extracting sequence from human genome hg19 by coordinates? i have millions of start-end positions, might this huge amount of data not suite for Table browser. I was think use the .2bit genome, any suggestions? i am also thing using following steps:
** * * *twoBitToFa* * twoBitToFa - Convert all or part of .2bit file to fasta usage: twoBitToFa input.2bit output.fa options: -seq=name - restrict this to just one sequence -start=X - start at given position in sequence (zero-based) -end=X - end at given position in sequence (non-inclusive) faToNib faToNib - Convert from .fa to .nib format usage: faToNib in.fa out.nib nibFrag nibFrag - Extract part of a nib file as .fa usage: nibFrag file.nib start end strand out.fa Is this would be the fast way? Thanks in advance. Best. * -- Daofeng Li Postdoc Research Associate Department of Genetics Washington University in St.Louis School of Medicine 314-556-2832 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
