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Recent Replies
Answer: Calculation method of RMSMappingQuality
by
zhoujun.nmu
•
0
Hello,
Have you solved this probelm?
Comment: PCA in gene expression
by
ali
•
0
Thanks for your help
Dear i.sudbery
I have been working on a project related to the correlation between genetic mutations and drug resis…
Answer: Using STAR for RNA seq-alignment.
by
LChart
2.2k
`genom_dir= ${pKS}/"star_index"` should read `genom_dir="${pKS}/star_index"` (n.b., no space after the =); inputFile and finput also need t…
Comment: RepeatMasker species error
by
jianzhi0515
•
0
check out this biostars question: it solved this issue of my repeat marker: https://www.biostars.org/p/488836/
Comment: No Passing Variants GATK
by
brandnewatthis
•
0
I ended up realizing it was a problem with bcftools - I didn't put my bgzip my vcf files therefore it couldn't read it. It looks to be fixe…
Comment: ExomeDepth installation error
by
jared.andrews07
★
14k
Again, no idea, I haven't used this tool. You will at minimum need a reference to compare your single bam file to, so I expect you'd need a…
Comment: No Passing Variants GATK
by
Pierre Lindenbaum
153k
> , or if the GATK error "unidentified variable MQRankSum" is causing this
try again without MQRankSum ...
Comment: PCA in gene expression
by
i.sudbery
16k
The noise on your differential expression is exactly the point. If samples are noise, then genes should be called differential.
Answer: Make a S4/S3 object with my clinical data
by
ATpoint
70k
Use a SummarizedExperiment. It's assay-agnostic so you can give any assay eith features/genes/observations as rows and samples at columns. …
Comment: TSS of protein coding genes
by
ConvolutedGenome
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10
I seeee
Thank you for your input :) !!
Comment: how to get to a VCF from bam files
by
Ram
38k
Read my script - change your bcftools to output VCF, not BCF. File size (as long as it's >0) is not an indicator of anything significant.
…
Comment: how to get to a VCF from bam files
by
Human
•
0
Thanks a lot GenoMax and Ram!
After a short look into that manual https://samtools.github.io/bcftools/howtos/variant-calling.html I went w…
Answer: BCFtools for somatic vs. germline variant calling
by
Ram
38k
bcftools does not differentiate. It calls variant loci. I don't think there's a single variant caller that calls both germline and somatic …
Comment: What means this Error when running a script in python??
by
Ram
38k
Please format your code properly the next time. I've seen people use wrong formatting options to a reasonable extent, but your formatting w…
Comment: Gaia CNV error TCGA data
by
Ram
38k
1. Don't use people's names as tags.
2. Format your post properly. I've done what I can for now.
3. Add a link to "the tutorial from @kevin…
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