[Genome] 3/5 UTR Sorting

Hello, If I download ETV6 from knownGene table and download the custom track for 5' UTR I was wondering what the data is sorted by. At first it appeared to be by the 5'UTR Exon start but with closer inspection this is not the case. Here is a snippet from my results: chr12 | 11187380 | 111874

[Genome] question regarding data field from Expression group track GNF Atlas 2

Hello, I want to know the definition of *qVal* and *hVal* from *gladHumESOtherData*table in *hgFixed* database. Thanks in advance. cheers Rubayte Rahman ___ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome

[Genome] BLAT axt vs psl ouput

Hi, I am using BLAT to align 454 reads back to an assembly that uses the same reads. I noticed that the axt output breaks across two alignments, while the psl output is within one line (see below). Is there a way to report the axt output as one alignment? Thanks in advance for the help. Vince

[Genome] snp135 vs dbsnp

Dear Sir/Madam, I want to download snp135.txt as for our GWAS studies. I found out that in this file that are multiple entries for one rs_id, just wonder which one should I use, why there are so many entries? e.g. rs74873759 Three entries in snp135.txt: 683 chr11292780212927803

[Genome] How to convert a UCSC gene name/alignID to a gene symbol gene name

How do I use R and possibly the BSgenome Bioconductor package to convert a UCSC gene name/alignID such as uc001bvd.3 to a gene symbol and gene name/description such as MARCKSL1 and Homo sapiens MARCKS-like 1 (MARCKSL1), mRNA? ___ Genome maillist - Gen

[Genome] quick question on SNP flanking sequences in table browser

Dear Sirs, I have a newbie-level quick question -- I'm looking at the table "snp135Seq", under the track "All SNPs (135)" in "Variation and Repeats". This table gives the rs number of the SNP, and a byte offset of the sequence in a fasta file. Apologies in advance for the simple question but: --

[Genome] 3'utr seq data

Dear Sir, I was wondering if there's a way to download only the 3'utr seqs of all human Refseqs from your DB Thank you Shirley Elias, Phd student Yoav Soen's group Weizmann Institute of Science ___ Genome maillist - Genome@soe.ucsc.edu https://lists.so

[Genome] q-value in SYDH TFBS track

Dear UCSC, We are using the SYDH TFBS track in UCSC hg19. The q-values of the peaks are claimed to take -log10. However, we found that the q-values of some files are quite small and are largely far from the corresponding p-values, such as wgEncodeSydhTfbsNb4Pol2StdPk. In this case are 117 files in

[Genome] SNP annotation

I am e-mailing if any tool has been created within UCSC genome browser that would allow the user to upload putative (novel) variants from NextGen data for annotation. I found one person asking a similar question 3+ years ago (see below) and was curious if this has been addressed since. Thanks

[Genome] Using problem

Dear Sir or Madam:   But I do know how to find the standard sequence of mitochondrial tRNA and rRNA, such as mitochondrial tRNAGlu(UUC) and 12S mitochondrial rRNA. I do not know whether the UCSC have thisfeature.   I shall be eagerly waiting for your mail. Da Li Chinamedical university ___

[Genome] Questions about Arabidopsis senescence eoigenome

To whom it may concern I am ilhwan, Lee at POSTECH in Korea. Thanks for your good website. I have a question. I read the paper that is published in 2012 March in PLOS ONE (Genome-Wide Evaluation of Histone Methylation Changes Associated with Leaf Senescence in Arabidopsis) And I fou

[Genome] Macaca fascicularis genome?

Dear UCSC Genome Project, I see from your FAQs that ~5 months ago the Macaca fascicularis genome was on your list of genomes to upload. Is this close to being done now? While we have uploaded this genome to our in-house UCSC browser independent of all other genomes we would like to have the con

Re: [Genome] hg19 phylop scores for mammals

Hi Promita, I noticed you are using our test server (http://hgdownload-test.cse.ucsc.edu) to download phyloP scores. Please note that our test server contains a lot of experimental and untested data, and this may be why you are noticing these discrepancies; the data displayed on our public br

Re: [Genome] UCSC genome browser to output sequence in FASTA format

Hi Christopher, Please see this previously answered question: https://lists.soe.ucsc.edu/pipermail/genome/2010-July/022912.html Please contact us again at genome@soe.ucsc.edu if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 3/29/2012 3:25 PM, Christo

Re: [Genome] SNP coordinates

Hi Rodney, We appreciate your comments. With regards to viewing SNP coordinates, this behavior in the web browser when you rollover items in the track display varies between web browsers. For example, Firefox and Internet Explorer display the URL at the bottom of the page, whereas Chrome does

Re: [Genome] hg19 phylop scores for mammals

Luvina MANY THANKS for the pointer Promita From: Luvina Guruvadoo [luv...@soe.ucsc.edu] Sent: Monday, April 02, 2012 1:19 PM To: Bose, Promita Cc: genome@soe.ucsc.edu Subject: Re: [Genome] hg19 phylop scores for mammals Hi Promita, I noticed you are using our tes

Re: [Genome] galGal4 assembly

Hi Mayela, Any preview downloads for galGal4 would be on our downloads-test site here: hgdownload-test.cse.ucsc.edu/goldenPath/galGal4/ However, only the 2bit file is currently listed. As we don't know when this assembly will be ready, I don't know when more downloads might be available. And k

Re: [Genome] quick question on SNP flanking sequences in table browser

Hi Sean, > which fasta file does this point to? /gbdb/hg19/snp/snp135.fa (Beware, it is a 29G uncompressed file.) >are line returns included in the byte offset count, or should this be interpreted as an offset of number of sequence characters into the chromosome sequence? They are byte of

Re: [Genome] How to convert a UCSC gene name/alignID to a gene symbol gene name

Hello, Pierre. You can actually accomplish this using our Table Browser. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. 1. From http://genome.ucsc.edu, select "Tables" from the blue navigation bar at the top of

Re: [Genome] SNP annotation

Hi Scott, We have recently begun work on a variant annotation finder tool. I don't have a time estimate for its completion, but it is under active development. If you have further questions, please contact us again at genome@soe.ucsc.edu. -- Brooke Rhead UCSC Genome Bioinformatics Group On

[Genome] Problems with Organism Info in gbCdnaInfo, e.g.AU194514

Hi, I am noticing problems in 'gbCdnaInfo' table in the Organism field. E.g. take the acc, AU194514. In NCBI it belongs to Porphyra yezoenis (taxid:2788), but in gbCdnaInfo table, the Organism field has taxid as 623 (Shigella) for this acc. This is not limited to just one record. It would be gr

Re: [Genome] Macaca fascicularis genome?

Hi Paul, The Macaca fascicularis genome is still on our to-do list, but there are several assemblies with a higher priority, so it will still be some time before we get to it (I don't have any time estimate for it). Good luck with your research. -- Brooke Rhead UCSC Genome Bioinformatics Group