Correction: /gbdb/hg18/snp/snp130.fa
On 5/10/10 1:34 PM, Jennifer Jackson wrote: > Hi Kyle, > > You should be able to rsync the entire file located > /gbdb/hb18/snp/snp130.fa and use it as-is. If you altered it after > retrieval, this could be the root cause of the indexing problem. > > Please try again with an intact file and let us know if the problem is > not resolved, > > Thank you, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/10/10 1:06 PM, Kyle Tretina wrote: >> To whom it may concern, >> >> I sent you an email some day last week, and have not been able to respond >> because of class finals week. As I said before, I am attempting to >> create a >> mirror of your website, using only chr16 and the snp130.fa to >> reproduce the >> alignments. When I enter in an rsnumber, the graphic with the rsnumber >> in a >> black box appears as expected. However, when I click on it to get to the >> next page that should have the alignment, I instead get the following >> error >> message: >> >> Expected FASTA header, got this line: >> tgcgg tgacgggcgc >> at offset 1632856238 in file /gbdb/hg18/snp/snp130.fa >> >> After re-downloading and re-loading the tables we are still getting >> the same >> error. >> >> I would like to find out if the snp130.fa file that you use is somehow >> different than what I have. If the file format is ascii and it is created >> for a windows environment the line endings are different than unix (eg 2 >> characters per line vs 1 character per line). I assume you are running on >> unix boxes. Could check to find out if your snp130.fa file looks the >> same as >> mine when I probe >> for rs8063034? >> >> Can you do an octal dump on the file /gbdb/hb18/snp/snp130.fa to see if >> you see the same or different than what we are seeing? - here is the od >> script >> ==== >> jo...@ubuntu:/gbdb/hg18/snp$ od -c -A d --skip=1632856238 snp130.fa | >> more >> 1632856238 t g c g g t g a c g g g c g c >> 1632856254 \n c t g t a g t c c c a g c t >> 1632856270 g c t c t g c a g g c t g a g >> 1632856286 g c a g g a g a a t g g t g >> 1632856302 t g a a c c c g g g a g g t g >> .... >> ==== >> If you see something different then I need to focus on the download >> process >> of the snp130.fa file - eg where I am getting it - how I download it. >> If you see the same thing then I need to find out why I am looking in the >> wrong place - if this is the case maybe you could include some >> debugging to >> show where I should be looking in snp130.fa for this rs number? >> >> Kyle Tretina >> Wheaton College >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
