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Dear masurca developpers, dear all
First of all, thank you very much for developing this very nice suite, very usefull for the community :)
I encounter a very long lag time of more that 15 days at t…
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## Documentation request
### Tool(s) involved
**CollectHsMetrics** \\
**--BAIT_INTERVALS** bait.interval_list \\
**--TARGET_INTERVALS** target.interval_list
### Description
Ther…
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I used the [data_mrna_agilent_microarray.txt](https://github.com/cBioPortal/datahub/blob/master/public/brca_metabric/data_mrna_agilent_microarray.txt) data from the portal
[brca_metabric](https://git…
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Hello, is there way to filter the SV's called by manta with ROI in bed format. Bedtools intersect cannot be used for the complex SVs. Does Manta has any in-built tool for this or will there be one any…
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Hi! It was my understanding that the GenTrain score is "project" dependent and does not come from the cluster file. Is this correct?
If so, what does the score calculated in the GenTrain.py module re…
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It would be extremely useful to provide users a way to manipulate the destination collection based on the source path.
For example, in the case of illumina sequencing runs, the start date is part o…
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Add genomic annotation to epimutations detected. List of proposed features that can be added:
- [x] Proximal gene
- [x] Gene position (i.e. promoter, body, 5'UTR...)
- [x] OMIM entries for proxim…
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Hi,
I incidentally poked over your project and I wonder why you keep track of `Average read depth` and of `Observed insert size`. The former would be better replaced with `Median read depth` and th…
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Base calling, is the systematic assignment of nucleobases to chromatogram peaks in case of electrophoresis, current changes resulting from nucleotides passing through a nanopore in case of Nanopore se…
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Hi I am using masurca (v3.2.6) assembler for assembly of plat with 1Gbp genome and I can observer quite high memory usage in command assembly.sh in line:
`create_k_unitigs_large_k -c $(($KMER-1)) -…