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8.1 years ago
onspotproductions
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150
I have some experimental data that was partial completed three years ago. Out of this data they originally got differential expression of genes. The issue I am having is reproducing this dataset. I took the raw data and mapped it to hg19 as they had done previously however I am unsure which ensemble gtf file to use in cuffdiff. I have tried a few and get no results because I assume since I am not using the correct one the gene locations are not compatible with the aligned reads. What is the original hg19 ensemble build number or what is the best way to identify the correct gtf file to use.
No results, nothing at all or not what you were expecting?
No results at all. log2 fold change shows 0 for every gene in every row
Quick check, your bam files and gtf contain the same chromosome notation? (chr1 vs 1)
That I know is one issue. I aligned everything to UCSC's hg19 assembly, but their table browser only produces ENST IDs in GTF format for that specific build.That is most likely why I got 0 for all the rows. Would it be simple enough to have a script run through the ensemble file and add chr before each chromosome number?
The chromosome names have to match between gtf and bam, so I guess that might already be a good start ;)