[Singer, Ruth A.]

Hello,

I am a PhD student working on a long noncoding RNA. I am trying to access public datasets from different cell types to determine the expression of my lncRNA. The lncRNA is called Paupar. Paupar is annotated and has the RefSeq ID: NR_117095.1. It also has Entrez gene ID: 103164605.

My question is why given its annotation in mm10 cannot I find it listed on the gene lists published by most studies.

Any help with this would be greatly appreciated.

Best,
Ruth

[Cath Tyner]

Hello Daniel,

Thank you for contacting the UCSC Genome Browser support team. I have noted that you have 2 questions. For your first question regarding the custom tracks intersection for S. purpuratus and Turkey, can you please tell me what problems you experienced? If possible, could you tell me what steps you took, or perhaps include a link to a session so that I can see the problem?

Regarding your second question, you could be experiencing a transcript version problem.

This id (NM_001146697) is on version 2 now, which is 8122

​nucleotides

 long.

​ ​

Version 1 had 8121 nucleotides in it.

​Your​

 rna file is talking about version

​ ​

1 and what we have in refSeqAli is version 2.

​ Please let me know if you require further guidance. ​

Thank you again for your inquiry and for using the UCSC Genome Browser. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private help: Email

 genom...@soe.ucsc.edu

UCSC Genome Browser Announcements List (email alerts for new data & software):

  * Subscribe: Email genome-announce+subscribe@soe.ucsc.edu 
  * Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu

Join us on Social Media! Facebook, Twitter, Wordpress Blog, YouTube

​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

On Thu, Mar 16, 2017 at 2:24 PM, Daniel Zhu <daniel...@gmail.com> wrote:

Hello,

I have been having trouble making custom tracks from 5' and 3' UTRs on the Table Browser and then intersecting it with a custom track I made for S. purpuratus and Turkey. There may be more that do not work but those are the first two I have encountered problems with. 

Also, I am working with FIMO MEME output in the form of .gff files for various organisms. When I was running this code for the chimpanzee FIMO output (P. troglodytes.gff), I encountered an issue when I got the last line with the pslMap command.  

$ faToTwoBit -stripVersion panTro5.rna.fa panTro5.rna.2bit
$ twoBitInfo panTro5.rna.2bit gene.sizes

$ awk '{gsub("\([*.]\).*", "", $1); print $1, $4, $5, $1}' P.\ troglodytes.gff > panTro5.bed
$ bedToPsl gene.sizes panTro5.bed panTro5.psl
$ mysql -u genome -h genome-mysql.cse.ucsc.edu -ANe "select * from refSeqAli" panTro5 | cut -f2- > panTro5.refSeqAli
$ pslMap panTro5.psl panTro5.refSeqAli panTro5.out.psl
I got this error message:
Error: inPsl NM_00146697 tSize (8121) !=mapping alignment NM_001146697 qSize (8122) (perhaps you need to specify -swapMap?)
I have also encountered this same error message when doing it with other organisms such as X. tropicalis.

Thank you so much for your help,

Daniel Zhu

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser discussion list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.

[Christopher Lee]

Hi Ruth,

Thank you for your question about the long noncoding RNA Paupar. This
mailing list is for questions relating to the data or software
produced here at UCSC, and is not a source of general scientific
advice. Since your question is about data external to UCSC, you will
have to ask the producers of the data why they did not include Paupar
in their studies.

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute