hmaarrfk
commented
3 months ago Conda forge is really only enable in ensuring the packages are installed correctly.
We aren’t really in a position to help support their usage from a scientific perspective.
try posting on their official channels https://github.com/nedialkova-lab/mim-tRNAseq
AteeshaNegi
Solution to issue cannot be found in the documentation.
Issue
I am trying to analyze the abundance, modification, and charging in tRNA of E. coli and mito tRNA of Human samples. When I use the following command for a human tRNA sample, the MimSeq code runs without any interruption. The command for MELAS sample:
mimseq --species Hsap --threads 16 --control-condition 0_Control -n mimseq_Melas_test --out-dir ./mimseq_MELASE_YN --cluster --cluster-id 0.95 --min-cov 2000 --max-mismatches 0.1 --remap --remap-mismatches 0.075 MELAS_samples.txtHowever, when I use the same command for E. coli, I encounter an error during the final deconvolution step. The command used is:
mimseq --species Ecol --threads 16 --control-condition EV_Control -n mimseq_A_bc1 --out-dir ./cluster_mimseq_A_bc1_test --cluster --cluster-id 0.95 --min-cov 2000 --max-mismatches 0.1 --remap --remap-mismatches 0.075 AlaGGC_A_bc1_test.txt > ./cluster_mimseq_output.logsError Log:
When I use the --no-cluster flag, I don't encounter this issue, but the alignment shows a high percentage of multi-mapping reads (Uniquely mapped reads: 48%; Multi-mapping reads: 48%).
With clustering, the uniquely mapped reads increase to 97%, but the run is interrupted and does not produce the final alignment folder, mod folder, or other output folders.
Questions:
1) What might be causing this error during the final deconvolution step with clustering enabled for E. coli? 2) Are there specific flags or parameters I should adjust to resolve this issue? 3) What is the significance of clustering in terms of isodecoders and overall tRNA modification analysis in MimSeq?
Any insights or suggestions to resolve this would be greatly appreciated. Thank you!
Installed packages
Environment info