Hi,
I am trying to run flair with multiple samples (same conditions, 4 different donors). I have followed the manual and concatenated the flair-corrected read bed files and fq files for the collapse step but don't understand my results. I have been trying to pick out the individual reads corresponding to each isoform so I can inspect them in IGV for possible associations with SNPs.
In the FLAIR collapse step, FLAIR appears to be generating the isoforms from just one of my samples and then looking for these in the other samples in the quantify step instead of generating isoforms by looking at all 4 samples. This is a problem for me as I am looking for novel transcripts. Is there a way to stop this from happening or to find the reads corresponding with each of the transcript isoforms for my other 3 samples?
I have read the paper (https://doi.org/10.1038/s41467-020-15171-6)
and the manual (https://flair.readthedocs.io/en/latest/) and I still have a question about
Hi, I am trying to run flair with multiple samples (same conditions, 4 different donors). I have followed the manual and concatenated the flair-corrected read bed files and fq files for the collapse step but don't understand my results. I have been trying to pick out the individual reads corresponding to each isoform so I can inspect them in IGV for possible associations with SNPs. In the FLAIR collapse step, FLAIR appears to be generating the isoforms from just one of my samples and then looking for these in the other samples in the quantify step instead of generating isoforms by looking at all 4 samples. This is a problem for me as I am looking for novel transcripts. Is there a way to stop this from happening or to find the reads corresponding with each of the transcript isoforms for my other 3 samples?
Thanks!