Hi All
I am doing DE analysis on the cow (healthy vs unhealthy).
I align the reads to Cow Ensembl database.
I found that two genes ENSBTAG00000000667 and ENSBTAG00000040244 are both DE but with different LogFC and Q-value.
However, from Cuffdiff result due to the gene.gtf file, the gene names are A6QPR4_BOVIN and A6QQR3_BOVIN repsectively from Cuffdiff result.
But when I want to change them to the Gene Symbol, I found that they are same gene name :'APOL3' .
Pls see the links below:
ENSBTAG00000000667
ENSBTAG00000040244
(1)Is this normal? Are they allele?
(2)What shall I do? Shall I leave them both or select the higher logFC ones?
(3)if ENSBTAG00000000667 is DE gene but ENSBTAG00000040244 is not DE, what shall I do?
(4)How about if I align the reads to UCSC genome? Is it better than Ensembl ?
Thank you!
I am doing DE analysis on the cow (healthy vs unhealthy).
I align the reads to Cow Ensembl database.
I found that two genes ENSBTAG00000000667 and ENSBTAG00000040244 are both DE but with different LogFC and Q-value.
However, from Cuffdiff result due to the gene.gtf file, the gene names are A6QPR4_BOVIN and A6QQR3_BOVIN repsectively from Cuffdiff result.
But when I want to change them to the Gene Symbol, I found that they are same gene name :'APOL3' .
Pls see the links below:
ENSBTAG00000000667
ENSBTAG00000040244
(1)Is this normal? Are they allele?
(2)What shall I do? Shall I leave them both or select the higher logFC ones?
(3)if ENSBTAG00000000667 is DE gene but ENSBTAG00000040244 is not DE, what shall I do?
(4)How about if I align the reads to UCSC genome? Is it better than Ensembl ?
Thank you!
Comment