Dear Mailing list, I have a list of interesting nucleotide co-ordinate positions from a UCSC GTF file (Organism: Sus scrofa, build: Sscrofa9.2). Now want the corresponding sequences for those co - ordinates, since my list would be a little bit big, I plan to download the chromosome sequences and get the sequences through ad hoc scripting or EMBOSS tools. But when I look at the sequence & annotation download page (http://hgdownload.cse.ucsc.edu/goldenPath/susScr2/bigZips/), I see several chromosomal fasta files. In that case, which chromosomal fasta file should I download to get the correct nucleotides for the positions in the GTF file ? ie should I download the chromosome assembly sequence file (chromFa) or the repeat masked (chromFaMasked)
Thank you in advance. Sudeep. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
