Luca Denti
Luca Denti
Ok, thanks! I'm working on genotyping SVs and, at least from the few examples I opened in IGV, it seems to work quite well: when I clearly see two alleles...
Oh, great! Thanks! Best, Luca
Hi Yan, I just extracted these two small fastas from some reads I'm working on ([hete-examples.zip](https://github.com/yangao07/abPOA/files/8067937/hete-examples.zip)): I extracted portions (substrings) of the reads covering potential heterozygous events (a deletion and...
Thanks Yan!! I'll check it out. Best, Luca
Hi, thanks! Just to be sure: in the event reads map to intron 19 as in Figure 1, right? If that's the case, ASGAL struggles a bit in identifying such...
I see your point. From the IGV screenshot, I can confirm that unfortunately ASGAL cannot detect that event. Indeed, you don't have any spliced alignments and all the events ASGAL...
Ok, got it! Thanks! Actually I just need the annotation and the reads falling on this gene (fastq used with asgal or the output sam). They should be small: you...
Hi, can you try running ``` python3 asgal.py -h ``` ?
Sorry, my fault, the script is `asgal`: ``` python3 asgal -h ``` (this from the root of this repo).
Great. I suspect it is due to the shebang https://github.com/AlgoLab/galig/blob/880811546525bb9c8afff44aea5ab375d0a33651/asgal#L1 Can you try to change it to ``` #!/usr/bin/env python ``` and try again with ``` ./asgal -h ``` ?