Hello, I would like to give you a question about the use of SQuIRE for the comparison of multiple RNA-seq data generated with different libraries.
I am performing the differential analysis of samples of data obtained with different libraries (first and unstranded). In the count step I indicate the type of specific library to correctly perform the TE quantification but when executing the differential analysis I obtain few significant differences due to the differences between both libraries.
When I remove the unstranded samples of the analysis it finish successfully and I have more consistent data. Is there a way to include this batch effect in squire?
Hello, I would like to give you a question about the use of SQuIRE for the comparison of multiple RNA-seq data generated with different libraries. I am performing the differential analysis of samples of data obtained with different libraries (first and unstranded). In the count step I indicate the type of specific library to correctly perform the TE quantification but when executing the differential analysis I obtain few significant differences due to the differences between both libraries. When I remove the unstranded samples of the analysis it finish successfully and I have more consistent data. Is there a way to include this batch effect in squire?