Dear ,
I have read the paper (Detecting haplotype-specific transcript variation in long reads with FLAIR2)
and the manual (https://flair.readthedocs.io/en/latest/) and I still have a question about FLAIR2 and HSTs
HSTs
Haplotype specific transcripts (HSTs) give me a feeling similar to the union of ASE and RNA editing. Is that the case. So once I use FLAIR2 to discover HSTs, I may be able to find potential Allele specific expression (ASE) or A-to-I?
FLAIR2
In the article (doi: 10.1186/s13059-024-03301-y), I noticed that you used Longshot to call variants in long-read data. Excuse me, if I perform NGS or long-read whole genome sequencing on this sample, can I use WGS to call variants and then combine the variants information with long-read RNA sequencing to identify haplotype-specific transcripts (HSTs)?
If I could do this, is it limited to long-read genome sequencing or can NGS also be used?
Dear , I have read the paper (Detecting haplotype-specific transcript variation in long reads with FLAIR2)
and the manual (https://flair.readthedocs.io/en/latest/) and I still have a question about FLAIR2 and HSTs
HSTs Haplotype specific transcripts (HSTs) give me a feeling similar to the union of ASE and RNA editing. Is that the case. So once I use FLAIR2 to discover HSTs, I may be able to find potential Allele specific expression (ASE) or A-to-I?
FLAIR2 In the article (doi: 10.1186/s13059-024-03301-y), I noticed that you used Longshot to call variants in long-read data. Excuse me, if I perform NGS or long-read whole genome sequencing on this sample, can I use WGS to call variants and then combine the variants information with long-read RNA sequencing to identify haplotype-specific transcripts (HSTs)? If I could do this, is it limited to long-read genome sequencing or can NGS also be used?
Can you give me some help? Thank you, bx