Entering edit mode
3.2 years ago
avelarbio46
▴
30
Hello everyone! I'm trying to run Star fusion on galaxy.org, but I'm not sure about what inputs this tool needs.
It requires a reference file (ok), a GTF file (ok, downloaded from gencode) and also the "Result of BLAST+-blastn of the reference fasta sequence with itself"
About this last one, galaxy recommends using the one obtained from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
But I'm not sure what is the input for this data. I tried with the plug'n'play 31gb file, but it fails. I download this 31gb human file, hg38, and unzipped in my computer. It is full of files and even countain other zipped files, but I have no idea which file I should use for this "Result of BLAST+-blastn of the reference fasta sequence with itself"
it's not that you can't post question about Galaxy here, but for more rapid (and perhaps accurate) advise I recommend you post this on the galaxy support forum: https://help.galaxyproject.org/
I tried, but there is no tutorial about it, and no information also. I got many errors, including one that I thought was server side, but the admin asked me to check my inputs and I have no clue on how to do so
as far as I understand (and without knowing the details of your 'issue') , that galaxy support forum is a forum like this one (biostars), where you can ask questions to the community, it's not only about tutorials.
It seems like the galaxy comunity is not on galaxy help. I tried to use one tool which had no tutorials, it didn't work and no one helped me there. This is the same with starfusion. I have been trying to run it for two months now, the first month the errors ammounted to some internal error (server-sided). They corrected it, and when I tried to run, I got not luck with many errors. It seemed like an input error, but there is no tutorial that I could find and the admin didn't help me, she just said to look the inputs and find what was wrong. The lack of tutorials and help in the online tool left me astounded, because STAR-fusion runs very differently offline than in galaxy. Offline, you need to build your data or use a plug'n'play file, but this plug'n'play does not work on galaxy online. I have been trying on trial and error to find this "Result of BLAST+-blastn of the reference fasta sequence with itself". I downloaded the 31gb plug n play file and found a tabular annotation which seems to be the correct input, but the lack of specification on galaxy side seemed very weird. Normally the datasets are very well defined and well writen so it's very hard to not understand what the input is