Hi,
AFAIK those tags appear in the quantification status of each object of each sample. I got this from the cufflinks manual http://cufflinks.cbcb.umd.edu/manual.html#tracking_format
Quantification status for the object in sample 1. Can be one of OK (deconvolution successful), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents deconvolution
it seems only objects with 'OK' should be taken into account but I don't know...
HTH,
marina
That's what I also found in the manual....but there is no exact definition! Because if i have a look at these genes in the genome browser some of them look really ok...not shallowly sequenced....bit strange :(
For example PE 2x65bp one condition mapped and quantified with tophat and cufflinks:
ACTG1 - - ACTG1 ACTG1 TSS22993 chr17:79476996-79479892 - - 1599.66 0 1866.02 FAIL
http://imageshack.us/photo/my-images/813/actg1.png/
does this look like a fail??
I had a detailed look at the 'FAIL' tag....only genes with different isoforms have this tag :/ Some are okay some not...so this means that cufflinks can not calculate exactly the abundance for all isoforms?? There is no 'FAIL' tag for genes with only one transcript variant!!
Could you edit tyour question adding the command you used? The isoforms with the FAIL tag have really low abundance?
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