User: Mike Vermeulen
Mike Vermeulen • 0
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Posts by Mike Vermeulen
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... I'm getting the same error but only when attempting to download specific SRR files.
If I try to download SRR files with DATASTORE_FILETYPE=cram I get the error "cant be found",
but if I download files with DATASTORE_FILETYPE=sra they download fine.
I have already set up access keys for GTEx data, ...
written 9 months ago by
Mike Vermeulen • 0
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Comment:
C: MAMBA ASE Software host site down
... I successfully installed the program using this source tree.
I still cannot find documentation but the help messages will have to do.
Thanks. ...
written 15 months ago by
Mike Vermeulen • 0
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... When following the GATK documentation for ASEReadCounter, the established tool for further analysis is MAMBA.
The link for [MAMBA][1] is broken and I can't find the program anywhere else.
Does anyone know if its hosted elsewhere?
[1]: http://www.well.ox.ac.uk/~rivas/mamba/ ...
written 16 months ago by
Mike Vermeulen • 0
• updated
16 months ago by
h.mon ♦ 28k
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... Hello everyone,
I have 12 singleton WGS samples that I am trying to phase using Shapeit2 using the reference panel method from 1000 genomes. I can successfully run the program and finish with a vcf containing estimated haplotypes for each variant. However, I'm looking for a confidence value on eac ...
written 18 months ago by
Mike Vermeulen • 0
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... Currently I have the allele-specific expression data on 12 different cancer types from TCGA.
I've organized them into matrices that consist of log2(alleleA_readcounts/alleleB_readcounts) for each gene for each patient
I've also converted this into a Z-score matrix (Z-score across each gene,) but I ...
written 3.2 years ago by
Mike Vermeulen • 0
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