Greg Boratyn

Yes, by default files created by docker container belong to root. This may be a problem if you do not have root permissions. These may be possible side effects: *...

Hi Juan, Thank you for using Magic-BLAST. This may happen when your reads contain a lot of repeats or you are aligning to a genome with alternative sequences. Magic-BLAST's threads...

Hello @pablomics-star, I am sorry you ran into problems. This error indicates that Magic-BLAST cannot parse the FASTQ file. It expects a new sequence with a defline at line 981584,...

Hi @asethi-1, Thank you for giving Magic-BLAST a try. Unfortunately we do not currently have any documentation for `-fr` and `-rf` flags. At this time they only work with the...

Thank you for reporting this. We need to do run a few comparisons between Magic-BLAST and STAR outputs to see what is happening. I will get back to you when...

Hi @sunriseTM, I am sorry you ran into trouble. Can you post an example? It is difficult to say anything without looking at the data. In general, Magic-BLAST is conservative...

Thank you for the example. Yes, intron detection is generally more difficult with long reads, because of increased error rate. It looks like Magic-BLAST overextended here on one side and...

Hi @joseailtoncruz, Thank you for trying out Magic-BLAST and I am sorry you ran into problems. How did you download the `SRR1237994.fas.gz` file? I suspect that it is in FASTQ...

@joseailtoncruz, could you post the exact error message for the run?: ``` magicblast -sra SRR1237994 -db my_reference ``` Please, also make sure you are using the latest version of Magic-BLAST:...

@joseailtoncruz , thank you for all the information. I am looking into possible fixes, but need to ask you a few more questions: 1. What is the error message for...