Question: libraries in SEQC
gravatar for siamak
3.7 years ago by
siamak0 wrote:

I am going to use RNA-seq counts provided by SEQC package to benchmark my method, however I am a bit confused about the final counts for each replicate. In each dataset, there are libraries from different lanes and flow cells for each group's replicate. My question is, should I add up the counts from all lanes and flow cells to obtain the final count for that replicate? For example, is the counts for replicate A_1 the sum of all A_1_L_X where L is lane number, and X is in {flow-cell1, flow-cell2}?




seqc • 546 views
ADD COMMENTlink modified 3.7 years ago by Wei Shi3.2k • written 3.7 years ago by siamak0
Answer: libraries in SEQC
gravatar for Wei Shi
3.7 years ago by
Wei Shi3.2k
Wei Shi3.2k wrote:

I believe I have answered your question in an email you sent me few days ago. But I just paste my answer here -


Dear Siamak,

Yes, the counts for A_1 should be the sum of counts from all its technical replicates. For differential expression analysis, you will need to use biological replicates to estimate biological variations. Technical replicates are not useful for this purpose and they should be added up.

Best wishes,

Wei Shi, PhD
Laboratory Head
The Walter and Eliza Hall Institute of Medical Research
Melbourne, Australia


ADD COMMENTlink written 3.7 years ago by Wei Shi3.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 309 users visited in the last hour