Hi, I have been trying to get reference data from the ucsc browser into Galaxy, but when I try to get the rat genome in gtf format, I only get files halfway through chomosome 10. This happens with both of the available builds for the rat. I am guessing this is a problem with the UCSC files and not Galaxy. However, I was wondering if you could perhaps help with this issue. When I try to get just chromosome 10, the gtf file halts in the same place as it does when I try to get the whole genome, with this message at the bottom of the file: chr10 rn4_refGene start_codon 4293086 4293088 0.000000 + . gene_id "NM_001008876"; transcript_id "NM_001008876_dup1"; --------------------------------------------------------------------------- offsetToGenomic: need previous exon, but given index of 0 --------------------------------------------------------------------------- Any ideas? I have no problem importing the "KnownGenes" option in UCSC - would this file work well as a reference - what is the difference in the different files from UCSC(ie. "gene and gene prediction tracks" vs "mRNA and EST tracks" or "KnownGenes" vs "RefSeq)? I guess I could try to download each chromosome separately to avoid that line in chromosome 10 and then concatenate them. I tried downloading the rat GTF from Ensembl, but when I brought it into Galaxy, it wasn't formatted properly, and didn't have the NM_0001 accession numbers associated with it but rather some other type of label, so it looks like it might need some grooming before use with the NGS suite. Thank you for any suggestions, David Martin dmarti@lsuhsc.edu
Hello Martin, A few other users had problems with this particular datasets last week when importing from UCSC. It was likely a transient problem, as "Get Data -> UCSC main" imports are working OK now from our test cases. Please try again and see if you can get the entire genome. Remember that "Get Data -> Bx main" is our mirror of the UCSC browser and can be an alternative source of data if there is some temporary connection/build issue preventing data import from UCSC main. Bx main can also be the best option if you want to get a large file loaded into a history quickly. About track content: The UCSC Browser's track description pages are the best place to get the details of construction. The quick distinction is that for the most part, the the gene group has finished sequences and the mRna/EST group has raw sequences. Please let us know if you need more help, Best, Jen Galaxy team On 2/17/11 12:34 AM, Martin, David A. wrote:
Hi,
I have been trying to get reference data from the ucsc browser into Galaxy, but when I try to get the rat genome in gtf format, I only get files halfway through chomosome 10. This happens with both of the available builds for the rat. I am guessing this is a problem with the UCSC files and not Galaxy. However, I was wondering if you could perhaps help with this issue. When I try to get just chromosome 10, the gtf file halts in the same place as it does when I try to get the whole genome, with this message at the bottom of the file:
chr10 rn4_refGene start_codon 4293086 4293088 0.000000 + . gene_id "NM_001008876"; transcript_id "NM_001008876_dup1"; --------------------------------------------------------------------------- offsetToGenomic: need previous exon, but given index of 0 ---------------------------------------------------------------------------
Any ideas? I have no problem importing the "KnownGenes" option in UCSC - would this file work well as a reference - what is the difference in the different files from UCSC(ie. "gene and gene prediction tracks" vs "mRNA and EST tracks" or "KnownGenes" vs "RefSeq)? I guess I could try to download each chromosome separately to avoid that line in chromosome 10 and then concatenate them. I tried downloading the rat GTF from Ensembl, but when I brought it into Galaxy, it wasn't formatted properly, and didn't have the NM_0001 accession numbers associated with it but rather some other type of label, so it looks like it might need some grooming before use with the NGS suite.
Thank you for any suggestions, David Martin dmarti@lsuhsc.edu
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