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mitochondrial SNVs are not called and integrated in Gsvar analysis platfom
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Snakemake code: https://github.com/imgag/megLR/blob/main/workflow/rules/cnv.smk
- [x] implement
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- [x] fix bug in mapping pipeline:
- [x] reads are lost during mapping
- [x] determine step and fix
- [ ] add check for sufficient file size/read count in mapped BAM
- [x] remove unmapped BAM …
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Hello,
I was able to install the megSAP pipeline and the NGSD database according to the instructions provided on GitHub and am now trying to run the trio_longread.php pipeline on our ONT data but cou…
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example: https://pubmed.ncbi.nlm.nih.gov/37081487/
[pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls]( https://pubmed.ncbi.nlm.nih.gov/37081487/)
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(base) [mmolla@dg-gpunode06 ~]$ modkit dmr pair -a /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/duplex_pileup.bed.gz -b /gpfs2/scratch/mmolla/Longread_1/SP2/SP2_A/CPG_duplex_pileup.bed.gz -o /gpfs2/scra…
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Hello, is this tool suitable for long read sequencing ?
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- [ ] on hold till we have enough diagnostic samples (300 Samples)
- [ ] check region of DarkMatter paper on LR data
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Combined ES + GS data/ short and longreads in a single project
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http://www.biomedcentral.com/1471-2105/15/211/abstract