Good morning Hiram, Thanks a lot for the reply and for the additional notification.
Regards, Sudeep. ________________________________ From: Hiram Clawson <[email protected]> To: sudeep s <[email protected]> Cc: "[email protected]" <[email protected]> Sent: Wednesday, 11 July 2012 6:56 PM Subject: Re: [Genome] GTF file nucleotide co-ordinates and Chromosome fasta files Please note this off-by-one correction: awk '{print $1,$4-1,$5,$3}' yourFile.gtf > coordinates.bed And if you are obtaining GTF files from the table browser, it would be much easier instead to allow the table browser to supply you with the correct BED file format without the awkward error-prone conversion to GTF format. Thank you Angie for the noted corrections. --Hiram Hiram Clawson wrote: > Good Morning Sudeep: > > Use the .2bit file, it has all the sequence and is masked. > Select out the coordinates (columns 1,4,5) from your GTF file to make > a bed file: > > awk '{print $1,$4,$5,$3}' yourFile.gtf > coordinates.bed > > Then use the twoBitToFa program to extract those sequences from the .2bit file > > twoBitToFa -bed=coordinates.bed susScr2.2bit result.fa > > --Hiram > > sudeep s wrote: >> 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
