Where To Download Refseq Mrna Sequence Data?

Question

[newDNASeqer]

I'm following this tutorial to create indicies of genome and transcripts at http://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial, but could not find the RefSeq from http://physiology.med.cornell.edu/faculty/elemento/lab/files/refGene.txt.07Jun2010.fa (the file is no longer there, throws a 403 error).

I have tried to google it, and found this NCBI ftp: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/, however, I'm not sure which file I should use for that tutorial. Can someone help me out? thanks

ps: I am trying to set up everything for doing exome-sequencing analysis (variant calling).

Answer 1

[Ashutosh Pandey]

You can use the following tutorial to create the missing file.

http://icb.med.cornell.edu/wiki/index.php/SNVseeqer/Adding_a_new_annotation_database

The starting refGene file for the tutorial can be downloaded from here:

http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=341054189&clade=mammal&org=Human&db=hg19&hgta_group=genes&hgta_track=refGene&hgta_table=0&hgta_regionType=genome&position=chr21%3A33031597-33041570&hgta_outputType=primaryTable&hgta_outFileName=hg19_refGene_table

Click on get output button.

Answer 2

[Charles Warden]

FYI, I think you only need the genome reference sequence.

There are some tools that require you to provide gene coordinates, but it isn't absolutely necessary. For example, you can use ANNOVAR to annotate SNPs without having to download an independent gene table. My own variant calling pipeline is BWA --> samtools (mpileup) --> VarScan --> ANNOVAR, and the gene location information is included as part of the ANNOVAR databases.

The aligner website will probably provide you with a link to the indexed genome files (although the BWA website isn't working for me right now). Illumina should also provide a download with several versions of indexed files for commonly used genomes (mouse, human, etc), but you might need an iCOM account:

https://icom.illumina.com/

You can also index your own sequence (from NCBI, UCSC, etc.), if you need to.

[Charles Warden]

Oh, I just re-read your title.

To clearify, you probably don't need the RefSeq information for DNA-Seq variant calling (using the pipeline that I mentioned above).

For RNA-Seq you probably will need a table of mRNA locations. However, I probably wouldn't remmend using BWA for RNA-Seq. You should use something like TopHat or STAR to handle the exon junctions.

Either way, you probably really want the coordinates rather than the mRNA sequences themselves.