User: Mike Vermeulen

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Posts by Mike Vermeulen

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Answer: A: sra toolkit prefetch: path not found while resolving tree within virtual file sy
... 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 Vermeulen0
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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 Vermeulen0
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MAMBA ASE Software host site down
... 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/ ...
expression asereadcounter rna-seq allele-specific written 16 months ago by Mike Vermeulen0 • updated 16 months ago by h.mon28k
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Phasing Confidence Values using Shapeit2
... 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 ...
haplotype estimation wgs phasing shapeit2 written 18 months ago by Mike Vermeulen0
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comparing log2 of allelic-imbalance (converted to Z-score) of different cancer types
... 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 ...
matrix z-score ase matlab rna-seq written 3.2 years ago by Mike Vermeulen0

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