It has a very good performance in the process of quantifying scRNA-seq data.Next, I'm thinking about whether it can be used to quantify the combination of genes and TEs.And I have tried this idea according to the following steps：
1.Change the classification information in the third column of the annotated TEs gff file to "gene" or "exon", and number all TEs as genes.
2.Merge genes and modified TEs files into a gff file.
3.After the transcript sequences are extracted, the index is established using the salmon index and the salmon alevin is used for quantification
The program can run normally, including subsequent analysis in R.
But I'm not sure if this is correct, so I would be very grateful if you have any suggestions！
Thank you for providing this good software！
It has a very good performance in the process of quantifying scRNA-seq data.Next, I'm thinking about whether it can be used to quantify the combination of genes and TEs.And I have tried this idea according to the following steps：
1.Change the classification information in the third column of the annotated TEs gff file to "gene" or "exon", and number all TEs as genes. 2.Merge genes and modified TEs files into a gff file. 3.After the transcript sequences are extracted, the index is established using the salmon index and the salmon alevin is used for quantification
The program can run normally, including subsequent analysis in R.
But I'm not sure if this is correct, so I would be very grateful if you have any suggestions！