Candida albicans gene counts

Question

[zad5zad]

Hi,

I'm asking how can I use the gene counts of Candida albicans on R for the DE analysis? because every gene has 2 versions A and B because C. albicans is diploid. Can I sum the counts from A and B together? Ex:

for rca1:

C1_00020C_A      9309
C1_00020C_B      11

for control:

C1_00020C_A   6973
C1_00020C_B    128

Thanks, Zeinab

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[WouterDeCoster]

Never mind you already changed the formatting...

[Ram]

I re-formatted it properly.

[GenoMax]

because every gene has 2 versions A and B because C. albicans is diploid

While that may be so I doubt that each one of your reads is able to tell them apart when you align them. In general people work with a single estimate of both copies for differential expression analysis.

Answer 1

[h.mon]

How did you count reads mapping to genes? Some programs (e.g. featureCounts and HTSeq) by default do not count multimappers, so you would be under-estimating counts if you used these programs. My suggestion is to use Salmon or RSEM, then summarize the counts with tximport, using a "transcript to gene" map which maps both versions of each gene to one gene. See previous discussions:

C Albicans Genome Count Matrix Total Genes

Generate a counts matrix with paired-end non-stranded samples

P.S.: another possibility is to analyse allele-specific expression, but then I don't have a suggestion on how you should proceed.