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Zkusit vzorek AED_106 (https://amtdb.org/sample/AED_106) prohnat pipelinou a porovnat výslednou mtDNA sekvenci s tím, co máme v databázi. Raw data vzorku: https://www.ebi.ac.uk/ena/browser/view/SAMEA1…
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Hi @danieljrichard, thanks for sharing this. Overall, I think the experiment looks good, and I can vouch for the workflow and clone calls. A few things to think about:
- I'm curious what the CellRa…
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Using mgatk to detect mitochondrial mutation sites in the mtscATAC-seq data (30x mean coverage of mtDNA) of mouse kidney tissue, I obtained low-quality mutations and genuine mutation sites, but did no…
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Hello! Thank you for making such a useful tool!
I am reaching out about an issue when using mgatk-del for other species. In the clifind.py file (mgatk--> deletion calling folder), it creates the c…
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## Bug report
Using storeDir makes the pipeline crash complaining that the required output file is not there any more.
### Expected behavior and actual behavior
In past storeDir was copying…
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Dear friends,
I have got a question from a reviewers regarding % of mtDNA reads of the total sequence reads that mapped to the whole mtDNA in MITObim. Where I can find this information in MITObim o…
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I used rCRS (NC_012920) as mtDNA reference sequence and received error as "Invalid fasta format: sequence size == 0". I also tried reference sequence file "chrM.fa" from MToolBox, and received same er…
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Currently, there are 2 problems with mtDNA display in Apollo:
- the gene page link outs don't work. They're set up to search for the Name attribute at NCBI. There are no name attributes for the fe…
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Hi Christoph,
Does MITObim subsample the input reads and how to get most of the input reads?
Is this read pairs or individual reads? "readpool contains 353396 reads" -see log file below.
[m…
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There is a mtDNA deletion in case 23103, which is not called in Scout. We have confirmed it with MLPA and also sequenced the breakpoints by sanger sequencing. I recently found mtDNA deletions in two o…