Sequencing depth and raw counts
0
0
Entering edit mode
3.5 years ago
glady ▴ 320

Hello,

If I have a sample sequenced in two different depths: 15-20M and 80-100M

1) How much difference will there be in the expression(raw count), of a certain coding gene coming from these two different libraries.

2) Is sequencing depth directly proportional to the read counts? If Yes, then how can we compare genes/features across samples having different sequencing depth?

gene ngs transcriptomics sequencing • 1.1k views
ADD COMMENT
0
Entering edit mode

is this your homework???

ADD REPLY
0
Entering edit mode

NO! I had this doubt bcz, when we download sequences from a open data source, the chunk of samples downloaded might be having different sequencing protocols.

So how good is it to compare a gene/feature across samples having different sequencing depth!

ADD REPLY
0
Entering edit mode

ok, answering your questions,

1) many low-expressed genes will be affected, highly expressed genes can be normalized but you will be losing many low expressed genes, the question is those missing genes are affecting the DEG analysis (and could be)

2) in genera yes, more reads means more expression, to compare the conditions you will need to normalize your libraries, R packages such as edgeR or DESeq2 have specific normalization methods.

ADD REPLY

Login before adding your answer.

Traffic: 1149 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6