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Recent Replies
Comment: Why isn't GWAS used in oncology?
by
Vincent Laufer
★
2.2k
Yes, but also .. I guess no.
First, there are familial cancer syndromes. Li Fraumeni, etc. runs in families. Thus, these are germline vari…
Comment: Ending up with only one BAM file
by
ATpoint
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You should get used right away to never work with uncompressed files. It just doesn't scale and takes up disk space which can be limited on…
Comment: Why isn't GWAS used in oncology?
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syntax
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Since LD deals with haplotype-inherited SNPs, I don't understand why LD has anything to do with cancer. Doesn't the presence of a tumor mea…
Comment: Why isn't GWAS used in oncology?
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syntax
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Right, I'm talking about producing an actual case-control association between each variant and the phenotype of interest using a tool like …
Comment: Ending up with only one BAM file
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for fq1 in /data/Data/*_R1_001_trimmed.fastq
you should use a workflow manager like nextflow or snakemake
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you're always using the very same output file whatever is the input in the loop.
--outFileNamePrefix STARpaired
use something …
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I had the same question - been trying to understand this for a while but can’t find anything :(
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You will need to inspect carefully your file as there might exist some lines with identical information. Check the attributes or show us sp…
Comment: Problem detecting indels
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Thank you Pierre.
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Seems like merging samples introduced some missing values.
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just because you found one read with a deletion doesn't mean that a variant will be generated. Now, it doesn't explain why there is not any…
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I have assigned unique IDs and attributes but still, it shows upload failed because multiple BioSamples cannot have identical attributes
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