Dear Lise, The N's are gaps. You can open up a gap track in the the Genome Browser to visually see these.
Hope this helps. If you have further questions, please contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "lise andrieux" <[email protected]> To: [email protected] Sent: Tuesday, March 8, 2011 9:31:29 AM Subject: [Genome] question about repeats in hg16 Hello, I couldnt find the answer therefore I am contacting you: I have downloaded data for chromosome 1 of hg16 from the downloads page, at http://hgdownload.cse.ucsc.edu/goldenPath/hg16/chromosomes/ It is written there: - chr*.fa.zip: compressed FASTA sequence of each chromosome. Each chromosome is in a separate file in a zipped Fasta format. Repeats -- which are shown in lower case -- are annotated by RepeatMasker run at the sensitive setting and Tandem Repeats Finder (repeats of period 12 or less). Repeats are in lower case, however in my data there are lower-case letter but also N, and as usually N is used to annotate repeats, I am now wondering what are the lowercase letters, if they really are repeats, or introns, and if they are repeats, what are the N ? Thanks for your help, Best regards, Lise Andrieux Lise Andrieux, PhD Life Sciences DPT Barcelona Supercomputing Center WARNING / LEGAL TEXT: This message is intended only for the use of the individual or entity to which it is addressed and may contain information which is privileged, confidential, proprietary, or exempt from disclosure under applicable law. If you are not the intended recipient or the person responsible for delivering the message to the intended recipient, you are strictly prohibited from disclosing, distributing, copying, or in any way using this message. If you have received this communication in error, please notify the sender and destroy and delete any copies you may have received. http://www.bsc.es/disclaimer.htm _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
