Open villegmb opened 3 months ago
Hi @villegmb,
Can you try removing the sample
column in your eventalign.txt
file and run xpore dataprep
again, please?
Thanks!
Best wishes, Yuk Kei
Hi @villegmb,
Can you try removing the
sample
column in youreventalign.txt
file and runxpore dataprep
again, please?Thanks!
Best wishes, Yuk Kei
Hello, I did it, but the outcome did not change. I got exactly the same.
Hi @villegmb,
I suspect that this has to do with how the gene_id (STRG.8) and transcript_id (STRG.446.1) look like in your fasta and gtf files. Can you try changing the gene_id and transcriptid to be separated with `instead of
.in your fasta, gtf, and eventalign.txt files as a
.is possibly recognized as
transcript_versionby
xpore dataprep`.
Thanks!
Best wishes, Yuk Kei
Hello. I am having problems with the output file from the dataprep stage. This is the code I am running:
This is my eventalign.txt file:
This is my gtf:![image](https://github.com/GoekeLab/xpore/assets/147038869/587edd3a-7afd-45f2-ac20-b60dc2b584be)
My Fasta:![image](https://github.com/GoekeLab/xpore/assets/147038869/56c1770b-fa27-4574-980f-10425f415856)
And my dataprep directory looks like this:![image](https://github.com/GoekeLab/xpore/assets/147038869/5000df30-d39f-40de-9bdc-1b947466f280)
Empty:![image](https://github.com/GoekeLab/xpore/assets/147038869/182d8350-0ac3-41d2-a547-606fc4afd71e)
data.json: empty
This is from the running process:
Can you please tell me what am I doing wrong?