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Recent Replies
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
GenoMax
142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA)
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ATpoint
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This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples
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DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes
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In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA)
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Thank you @atpoint, I did already investigate this error on the DADA2 github.
It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq
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Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA)
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One cannot help you with this. The error is from R, yet you show not a single line of R code.
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I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
Comment: Subsetting and merging back Seurat Object brings different results
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Ok I think I know what happened. The order of cells changed, otherwise its the same:
, and it has really good results. You might have a try.
https://githu…
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bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
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It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
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liorglic
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I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
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If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
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Thank you so much. I'm new to this and didn't realise there was a code option.
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