Hi Asaf, To find out which genbank or refseq entries didn't align by looking in the gbStatus table. The field of interest to you would be numAligns with the value of 0. Here is a link to the schema for the hg19 gbStatus table:
http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_doSchemaDb=hg19&hgta_doSchemaTable=gbStatus You can either use the table browser ( http://genome.ucsc.edu/cgi-bin/hgTables) to extract this information or if you are familiar with mySQL you can use our public mySQL server: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 Here is an example mySQL query: select count(*) from gbStatus where srcDb="GenBank" and type="mRNA" and orgCat="native" and numAligns=0; Hope this helps you get started. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Asaf Levy <[email protected]> Date: Mon, Oct 31, 2011 at 7:21 AM Subject: Re: [Genome] Unaligned transcripts To: [email protected] Hi, I asked the question below 4 days ago and I did not get a reply. Do you hold a file of the sequences of unaligned human ESTs and cDNAs? Regards, Asaf On Thu, Oct 27, 2011 at 11:07 PM, Asaf Levy <[email protected]> wrote: > Dear Sir/Madam, > Let's start by admitting that I am a great fan of the UCSC genome browser > for the last 6 years... > > Since I know you guys download ESTs/mRNAs routinely and align these to the > human genomes, I'd like to know if it's possible to get from you a file of > all those transcript accessions or sequences + metadata (e.g: tissues of > origin) that you failed to align to the human genome. > > Regards, > Asaf > > -- > Asaf Levy, PhD student > Rotem Sorek Lab > Weizmann Institute of Science > Rehovot 76100, Israel > Tel: +972-8-9346344 > Cell: +972-54-7290026 > [email protected] > [email protected] > -- Asaf Levy, PhD student Rotem Sorek Lab Weizmann Institute of Science Rehovot 76100, Israel Tel: +972-8-9346344 Cell: +972-54-7290026 [email protected] [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
