Hello, In the latest versions of Eager, the mtcapture mode is no longer available, unless I'm mistaken. I would like to retrieve reads from the mitochondrial genome only and not reads that have moved to the nuclear genome to avoid artificial variants. How can I find reads that map only to the mito and not the nuclear? Second question: when I launched Eager with the mitochondrial genome, everything went smoothly. But when I ran it with the whole genome, I got this error message at the mtnucratio step: Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1 at MTtoNucCalculator.getMTLength(MTtoNucCalculator.java:143) at MTtoNucCalculator.<init>(MTtoNucCalculator.java:52) at MTtoNucCalculator.main(MTtoNucCalculator.java:71) Thanks for your help. sarah

The second error might be because there are no other Nuc reads to calculate the ratio on

Thanks, I will try with mteGenome

@Selina Carlhoff @Thiseas C. Lamnidis do you maybe have any suggestions?

Hi Sarah! eager What do you mean mtCapture mode is no longer available? What version are you using, and what sort of error suggested that is not supported? It should be possible to map to the full genome, and only keep mtDNA reads after mapping, by using

--mapper 'circularmapper' ----circulartarget '<NAME_OF_YOUR_MT_GENOME_IN_REFERENCE_FASTA>'

and specifying

--circularfilter

, which will filter out any reads that did not map to the circular genome. The relevant options are documented here: https://nf-co.re/eager/2.5.2/parameters/#mapping You will then need to ensure you do NOT run MtNucRatio (

--run_mtnucratio false

), as once all nuclear reads have been filtered out, that will cause a division by 0 errors. 🤔

@Thiseas C. Lamnidis she means compared to eager1

oh, i see. hopefully my reply was still somewhat useful. I have limited to no experience with EAGER 1