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Answer: How to compare compare two Sam files to check mapping
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Curious if others have also benefited from Picard's [CompareSAMs][1] tool. Seems to do exactly what Madhu has requested. If the headers …
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alex.zaccaron
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The best repository is probably NCBI Organelle Resources. You can search by taxonomy and download their mt genomes. Check it out for fungi…
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Good place to start looking: https://www.ncbi.nlm.nih.gov/genome/organelle/ Mitochondrial genomes may also be included in full genomes so …
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Nicholas
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Thank you! I will give it a shot
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This has been issued a dozen times before. Have a look at Limma package. https://support.bioconductor.org/p/126817/ https://support.bioco…
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Without your code, it is impossible to make any statement. Please provide the code generating that issue. By googling, here is a [similar …
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Hi, thanks for your information. I am a bit confused now. Does this mean the cram file already contained reference genome information? I in…
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> None of the requested assays are present in the object Does the assay `originalexp` exist in your object `seurat_from_cds` ?
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When calling for SVs using gridds, should I use the reference genome that I added my transgene to, or should I use the unedited reference?
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Thank for the reply. I am running this code: # set a set of soft-thresholding powers powers = c(c(1:20), seq(from = 22, to=30, by=2)) # Ca…
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prifa
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thank you for your reply Zepper, a bit clarification, I took all the samples from SRA data table, but yes from different lab and also diffe…
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That you have a varying number of replicates is not ideal ([see here why][1]), but manageable. See for example the [Specific experimental d…
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OK, in that case it should be even easier as its just a single pairwise alignment, so the same advice holds.
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Hi, Can you please share how did you clip both ends of the reads with ClipReads? Clipping form the start with `-CT "1-3"` for instance wor…
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