Is it possible to run Mipgen on a different organism (fasta)?
Flope opened this issue · comments
Hi,
I tried to run mipgen on a mouse but I noticed that I am getting the same svr score for every MIP (-3.81195) and the arm copies are suspiciously always 0.
I also tried with Saccharomyces and I am getting again the same scores (-3.81195) and arm copies (0).
It works fine for the human genome.
Is that expected?
If I am using...
-score_method mixed: I am getting the constant score.
- logistic scores: I am getting "nan"
- svr score: the program seems to run forever.
thanks,
Francesc
thanks Evan for replying.
Yes. I checked all that.
I used different regions for both mouse and Saccharomyces.
The MIPs are designed and it seems they may work.
However, the scores and arm copies seem to be wrong.
I am not going to be able to do proper testing in the following days but I could try single chromosomes for human and mouse and try to pinpoint the issue.
Have you tried other genomes or fasta files?
Thanks Evan.
In case somebody reads this:
As Evan found, It was a problem with the BWA index as clearly the error logs indicated and I missed:
[bwa_aln] fail to locate the index
[bwa_sai2sam_se] fail to locate the index
The sequence was collected using samtools faidx, but bwa were not able to map the sequence to the reference.