2 small and related questions

[Fawzi Yassine]

Hi,

I am analyzing public RNA-seq data to find genes differentially expressed between diseased patients and controls. The paper for which thepaper  belong says: ” The reads were mapped to human genome (hg19) by TopHat. The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser) was enumerated….”

 

Q1: Are  the 2 files compatible? (one file used for Mapping using UCSC hg19 Genome but another file used for annotation was downloaded from TableBrowser using track Refseq )

Q2: which track shall I use? ‘NCBI Refseq’ or ‘Other Refseq'.

Thank you,

 

 

 

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Fawzi Yassine, MS
Department of Computer Science
The University of Western Ontario
London, Ontario, Canada

 

[Conner Powell]

Dear Fawzi,

Thank you for using the UCSC Genome Browser and for your questions about file compatibility and RefSeq track selection.

To answer your first question, if you using Table Browser and select hg19 and any corresponding RefSeq track, the files will be compatible.

To answer your second question, the 'NCBI RefSeq' Genes composite track is made up of multiple subtracks. The subtracks are described below:

RefSeq annotations and alignments
RefSeq All – all curated and predicted annotations provided by RefSeq.
RefSeq Curated – subset of RefSeq All that includes only those annotations whose accessions begin with NM, NR, or YP.
RefSeq Predicted – subset of RefSeq All that includes those annotations whose accessions begin with XM or XR.
RefSeq Other – all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the RefSeq Curated or the RefSeq Predicted tracks.
RefSeq Alignments – alignments of RefSeq RNAs to the human genome provided by the RefSeq group.
RefSeq Diffs – alignment differences between the human reference genome(s) and RefSeq transcripts. Note: track not currently available for every assembly.

UCSC annotations
UCSC RefSeq – annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the human genome.

To learn more about The 'NCBI RefSeq' Genes composite track, here is a link to the description page: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refSeqComposite

The 'Other RefSeq' track contains tables with gene alignments and pseudogenes from species other than Human. You can read more at the description page here: https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=hg19&c=chr21&g=xenoRefGene.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Conner Powell
UCSC Genomics Institute

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Conner Powell

UCSC Genomics Institute, Quality Assurance and Support Analyst