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Recent Replies
Answer: How goes gene length effect the number of reads mapped
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See my answer about the what hows and whens of RNA-seq normalisation here:
https://www.biostars.org/p/9586553/#9586566
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Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
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See my post here for more details on RNA-seq normalisation:
https://www.biostars.org/p/9586553/#9586566
In short, TPM normalises for ge…
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I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
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Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement?
You could accept (green check mark) this…
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Thank you. My budget is around 20 thousand dollars.
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Prefetch files using sratoolkit **prefetch** command and then use **fasterq-dump**. There you can see the number of reads. For validation, …
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random downsampling of bam files is now possible using [rasusa][1] [v1.0.0][2] with the `aln` subcommand
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Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
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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…
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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…
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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…
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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…
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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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