Top new questions this week:
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I have tried to use UpsetR to visualize the input file which can be found here. …
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Is there a way to submit data to ucsc genome browser for result/track display, on the fly, as a local bedgraph file with example contents like below: …
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The code I ran was here, so nothing fancy. breseq -l 110 -o RifR_align -r Big_burk_assembly.fasta RifRNano_nanopore.fastq.gz This was the output. …
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I was wondering if somebody here has experience with installing scvi-tools on a Mac with M1 chip. I tried the following command: …
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I have a question related with the most popular frameworks for network construction: WGCNA for weighted networks and igraph package for unweighted networks. What are the advantages or disadvantages of …
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When trying to run epi2me-labs/wf-artic, I get the following error: …
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I want to perform Differential Gene Expression Analysis. I recently completed RNA Sequence Analysis using the Seraut Tutorial up to this point: Finding Differentially Expressed Features (Cluster …
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Greatest hits from previous weeks:
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I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, “recount_mdat.csv”)] when I tried to export the ‘mdat’, I got the following error: <...
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I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R. Samtools/BCFtools (Heng Li) provides a Perl script …
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Coming from a CS background. Reading through the wikipedia page, these all sounds like the same thing: Variant, Allele, and SNP. Variant/Allele/SNP: Some gene locus that differs from the idea human. …
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I would like to set the folder in which MinKNOW writes the raw data. How can I do this? I do not currently know where MinKNOW will output my data. What is the default directory where MinKNOW outputs …
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I am working with over a million (long) reads, and aligning them to a large genome. I am considering running my alignment jobs in parallel, distributing horizontally across hundreds of nodes rather …
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I have an R package on github which uses multiple Bioconductor dependencies, ‘myPackage’ If I include CRAN packages in the DESCRIPTION via Depends:, the packages …
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I’d like to learn which format is most commonly used for storing the full human genome sequence (4 letters without a quality score) and why. I assume that storing it in plain-text format would be …
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Can you answer these questions?
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www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117872 I’m teaching myself sequence analysis. This is the count data: and then this is, what I believe to be, the coldata: All I want to know is …
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how to make input data file for circos gene density visualization from gff file like this: output: …
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I’m pretty new in bioinformatics. I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I’d rather do this through via code than download …
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