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Has anyone else noticed that the GTF files in the Illumina iGenomes collection don't conform to the GTF specification ? The attribute list must begin with gene_id then transcript_id whereas in the iGenomes GTFs it is gene_id then gene_name then either p_id or transcript_id. It would be nice if those extra attributes were at the end of the list so they worked with more programs.
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Yeah, well Illumina has always been known about going off on their own. In any case I question a program that can not parse an arbitrary field. If the order of the attribute list *must* be in a given order then the specification should have just made room for two more exact columns instead of relying on programs to do the parsing. -
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Even though it's described as being ~5G, the actual download is ~9G.Originally posted by fongchun View Post
Do you also get 0 FPKM when you use the GRCh37 from the Tophat site?Comment
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Yes. I tried both the iGenome GRCh37 packages downloaded from Tophat and Cufflinks and both genes.gtf file gave me 0 FPKM for all genes when I just used cufflinks with the -G parameter.
It seems that maybe the current archive version (archive-2011-08-30-22-38-04) doesn't work? Anyone else have problems?Comment
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It took me a week to drill back through my pipeline and work out these files were messing it up. In the end I got a fresh genome and GTF from ensembl, then used custom scripts to build all the various files req'd for picard, GATK etc. Its now working like a dream.
Lesson - if it looks too good to be true...@sidderbComment
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I actually ended up somewhat solving the issue. It had to do with my .bam files having have my chromosome number appended with "chr". While the GTF files, didn't have the "chr". Thus when it tried to quantify the expression it was as if there were absolutely no alignments to the genome. Was frustrating to figure this out.Originally posted by sidderb View Post
Lesson - check to see if "chr" is appended to the chromosome number or not when dealing with datasets.Comment
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