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My "issue" is that I'd like to use vg to construct a pan-genome graph with annotated paths for each biological sample that was used to create that graph. My simple example is attached.
[ecoli.pan3.ta…
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Dear Jason,
Hello!
Can you briefly explain input_bam.fofn contents ?
How can I generate it ?
Thank you.
Won
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I try to insert two snv close-by but i see that only the second one is correctly inserted. The first one is not inserted on the reads that also cover the second position. (cf image)
I found a work-…
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Hi, I got all files empty after 48h running for 130* draft genome, version is 0.10.1. Here is all the commands:
$nanopolish index -d fast5_files/1 -d fast5_file/2 -s summary1.txt -s summary2.txt fi…
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This is closely related to https://github.com/jts/nanopolish/issues/235 but not identical, I therefore create a new ticket.
quite some background info:
* my genome is a bacterium, so it is haploid…
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I have successfully run FALCON using PBS here at MSI (https://www.msi.umn.edu/queues). However, we just upgraded to the newest FALCON and Unzip versions and I am no longer able to run the assembler.
…
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When a VCF file is imported SeqArray reads and use the default ref/alt alleles.
However, when samples are removed, depending on MAC/MAF, ref/alt alleles might change ...
**Question**
Is there a q…
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the current version of crispor seems to calculates the guide cfd score but doesn't print it to the output. Instead only the MIT specificity score and number of off-targets is printed. Would you be abl…
genya updated
5 years ago
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In `vg gbwt` we have code to merge GBWT indexes. But the code that uses GBWT indexes for haplotype-aware mapping reads the haplotype count from the *xg*, which it assumes was generated alongside the g…
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Hi,
I am using GATK `version gatk4-4.0.6.0-0` as part of the bcbio-nextgen pipeline for RNA-seq variant calling. There is one step in the pipeline i.e. `gatk GenomicsDBImport` that's been failing c…