Error in IGV "Cannot find feature or locus: RP11-571E6.3"

Question

[Y Tb]

I am trying to visualize mapped data that I got from Tophat for RNAseq data using IGV, and I am looking to specific genes names on this data. I can visualize some of these genes but the other no and I got this error message in IGV

Cannot find feature or locus: RP11-571E6.3

BTW: I am using hg19 as reference.

Answer 1

[Antonio R. Franco]

How do you know for sure that this gene name is included in hg19?

It is likely that this gene name could have been replaced from previous version

[Y Tb]

Dear Antonio, I used hg19 as a reference in Tophat, in addition, I used the gene model (annotation file .GTF file ) from ensemble . That is why I am looking for those genes names in my mapped data.

[ravi.uhdnis]

Hi, I am also facing the same problem. Was you able to find the solution?. If yes, please let me know. Many thanks, Ravi.