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Hello,
I just test pggb on a simulated data. I simulated a reference file(.fasta), the length of this reference is 3941bp. Then I simulated a query file(.fasta),the length of this query is 600bp. Th…
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Hello,
EAGLE-RC seems like a very useful tool for Allele specific expression.
I saw the option `--dp`. So with this is can run EAGLE-RC on aligned long-read RNA-seq (e.g IsoSeq)?
Or do you ha…
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I have four F0 (grandparents) fish strains A, B, C and D. A was crossed with B (AxB) and C was crossed with D (CxD) to give F1. The F1 (AB) and (CD) were then crossed AB x CD to give F2 generation (A…
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These are the commands I am running:
tools/star/STAR-2.7.10b/source/STAR --runThreadN 16 --runMode genomeGenerate --genomeDir GRCm38_index --genomeFastaFiles GRCm38_reference/GRCm38.primary_asse…
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Hi, I would really appreciate your help.
Even though, I read through all issues related to ploidy and purity adjustment, I'm still confused.
1. Based on one of the issues #40 , you mentioned that…
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There is a error when I using ASCAT analysis WES CNV.
Error in !is.null(homsegs) && !is.na(homsegs) :
'length = 3' in coercion to 'logical(1)'
Calls: ascat.aspcf
`
if (F){
ascat.prepare…
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Hi, thank you for creating **figeno** and making it public. It is very useful for me.
I would like to ask you some suggestions.
- Could you let me know if it is possible to plot inverted BigWig …
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Hi!
I have two separate vcf files for a **tumor** sample, one for indels and another for snvs. Both have been VEP annotated and decomposed. The **indels vcf** file has different variant callers:
Var…
ne1al updated
5 months ago
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I think the title says it all, but `DPA1*01:05` is present in the protein and cDNA/codon alignments, but is (inconspicuously) absent from the gDNA alignment.
![image](https://github.com/ANHIG/IMGT…
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Hi I'm trying to run nPhase on a tetraploid yeast genome I seqeunced with PacBio HiFi reads.
Here is my code:
`nphase pipeline --sampleName trialRun1 --reference s288c.fa --longReads pacbioHiFi…