As per the manual StringTie can be used with --merge in order to generate a non-redundant set of transcripts observed in all the RNA-Seq samples assembled previously. The stringtie --merge mode takes as input a list of all the assembled transcripts files (in GTF format) previously obtained for each sample, as well as a reference annotation file (-G option) if available. I have a few questions on this.
- I have 60 samples from Rat, 10 different organs and has 6 technical replicates for each organ. What is the best way to --merge? all the 60 samples at once or separate --merge for each and every organ.
- What is the significance of -- merge with an example.
- what is the next step after merging?
Thanks
Thank you for this helpful explanation and suggestion too.
No problem. If you like it you can always give it a thumbs up :-)
Sorry, I just forgot, I would love to do that. Thank you.