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Comment: Ideal PC configurations and operating system for bioinformatics laboratory
RNA-seq power estimation using ssizeRNA program
Answer: WGCNA preservation analysis
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
ISCN annotation for SV/CN VCF files
Comment: How to convert plink files to Hapmap Format
Am I crazy, or are most published RNA-seq studies vastly underpowered?
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Answer: Including plasmid in transcriptome assemblies
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GenoMax
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> I want to use both STAR and BOWTIE2 for assembly Those programs are aligners not assemblers. But since you are working with bacteria yo…
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I already have gvcfs called by chromosome and there are 24 gvcfs per sample which I merged them into a single gvcf per sample. Now I want …
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bk11
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First, could you please explain any reason for not using Seurat V5 approach for your data integration mentioned in [here][1]? > Now moving…
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So I'd take the json file located [here][1] and essentially create the whitelist to be all possible combinations of the position 1-10 barco…
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Hey Gnana, could you find a way to solve the issue? I have the same error
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
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You simply need to make a list of barcodes one on each line: https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-wh…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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> What specifications and operating system would be ideal for my case? For choice of OS: Linux to access the large pool of open source sof…
Comment: How to convert plink files to Hapmap Format
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bk11
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Ok. First update your phenotypes because in the 6th column all the values are -9 meaning missing, and then run `--assoc`. You can do the fo…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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i.sudbery
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You'll probably get away with using one of the other analysis pipelines, like Alevin-fry with much less than 128GB of RAM. Workstations can…
Comment: Difference between samtools "-f 9" and "-f 11"
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Dylan
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> (which is weird, if it's in proper pair, read and its mate should be both mapped) So that was my thought as well, I think the code you l…
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> several single cell samples At the same time? You need a server, not a PC. Google around (and search the site as well with keyword "conf…
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the data is binary and associated with a disease but we're studying only the cases and there are other phenotypes of severity
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could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or do you have to re-format the…
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> I didn't do a good job with Trimmomatic for some reason so I have to do some trimming of my transcripts. If you had extraneous sequence…
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