What does this "=" class code mean? If it means that the gene in the new model should be "=" to the original, is there any reason why some cases did not match the original model 100%, yet they still were assigned an "=" code?
people need more information. are you talking about a programming language, a curated gene database?
A little context would be helpful. Are you referring to a specific software or database?
if you compare two values in awk: $1 == $2 (or number) and $1 = "STRING" -- if you think this...100% match
does anyone know how to attach a screen shot?
You upload the image somewhere and then link to it.
Have you read the cufflinks documentation where this is described?
yes I did read it and it says it should be a complete match, but this is what seems to be occurring: (I'm not sure if the photo will be very clear!)
The top line is using tophat for alignment and the middle is using star for alignment. The bottom line is the original model, to which the top two should both be "=" to according to the cufflinks documentation. But in this case, the star model is not displaying an "=" to original image, when it is labeled as such. It looks as if there are multiple genes overlapping?
Warning NSFW: this tinypic service "decorates" the uploaded screenshot with other irrelevant photos, some of which may be inappropriate in a professional setting. People get fired for this kind of things. Please edit your post and add the screenshot inline.
I took the liberty of modifying things accordingly.
It would be rather helpful to see the GTF lines for the various cases, rather than an image.
If you notice the arrows are going different directions near the exon in the second track, that looks like overlapping features obscuring the view. Right click and go to "expanded" and you'll see the long one and the short one, which is probably equal.
amazing, thanks so much!
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