I have a 10x dataset with a transgenic gene which sequence is not available. A colleague has kindly sequenced the gene using Sanger sequencing and trimmed the sequence for me. It is not a full length sequence - only about 500 bases at the end.
2 Questions:
1. Can I get a reliable count of this transgenic gene if I just create a custom reference files with this sequence and run cellranger count? The sequence is very high quality (having looked at the chromatogram). The fact that it is not a full length sequence might compromise it?
2. What is the best way to retrieve the entire cDNA sequence from the 10x data I have on hand?
I'm very new to the sequencing world. So please be gentle.
2 Questions:
1. Can I get a reliable count of this transgenic gene if I just create a custom reference files with this sequence and run cellranger count? The sequence is very high quality (having looked at the chromatogram). The fact that it is not a full length sequence might compromise it?
2. What is the best way to retrieve the entire cDNA sequence from the 10x data I have on hand?
I'm very new to the sequencing world. So please be gentle.