Comments (2)
Hi,
the files in logs/ASGAL
contain what ASGAL outputs to stderr (if everything worked, all those files should be empty, otherwise they should contain information on what went wrong).
In that folder you can find a file for each gene that is processed by asgal: if we think we have at least one read on a gene, than you will find a file for that gene. In genomewide mode, salmon is used to perform transcript quantification and then the reads used to quantify the transcripts of a gene are "assigned" to that gene and mapped to its splicing graph.
I hope this may help you. Let me know if you have other questions.
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Thank you!
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