Regression model for the T>C rate in old RNA
Make sure that you either have samples without 4sU to let GRAND-SLAM estimate the regression model from these data, or to have the regression model for you protocol/sequencer. For the former, make sure that the names of the conditions (i.e. given in the metadata of the CIT file, or by the name of the BAM file) include "no4sU" (or, alternatively, use the -no4sUpattern parameter to tell GRAND-SLAM how to identify them). For the latter, specify it via the -errlm parameter.
But I did not do no4sU sequencing. I did 0h, 4h, and 8h treatment groups, and then used 4sU labeling for the same time for the three groups and then performed total RNA sequencing. I ran gedi -e Slam to get the tsv file, and conducted maplot and gsea analysis with grandR. I did not have samples of no4sU, so what was the impact of this? I just wanted to know the gene expression after treatment, and grandR has indeed got the result I wanted.
Hi，
I saw the following on the wiki:
Regression model for the T>C rate in old RNA Make sure that you either have samples without 4sU to let GRAND-SLAM estimate the regression model from these data, or to have the regression model for you protocol/sequencer. For the former, make sure that the names of the conditions (i.e. given in the metadata of the CIT file, or by the name of the BAM file) include "no4sU" (or, alternatively, use the -no4sUpattern parameter to tell GRAND-SLAM how to identify them). For the latter, specify it via the -errlm parameter.
But I did not do no4sU sequencing. I did 0h, 4h, and 8h treatment groups, and then used 4sU labeling for the same time for the three groups and then performed total RNA sequencing. I ran gedi -e Slam to get the tsv file, and conducted maplot and gsea analysis with grandR. I did not have samples of no4sU, so what was the impact of this? I just wanted to know the gene expression after treatment, and grandR has indeed got the result I wanted.