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Recent Replies
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ATpoint
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Please show relevant code. This is almost certainly some issue with the GTF.
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Personally, I feel this would not only depend on the experiment (which would be a large factor), but also what sort of thresholds and filte…
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I want to stress here (as I did in many posts before) that methods like harmony do a per-cell batch correction. This means the method aims …
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Yes, this interaction term would capture genes where the difference between day and night is altered as a consequence of genotype. Note tho…
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Can you try running each part/command manually on the command line (instead of the bash script) to see if there might be an error/warning t…
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Find out if your library protocol is stranded or not. If standed then these two genes should be independent. If not stranded then they shou…
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Ok, that's quite common but can cause a lot of fuzz (if you notice it, even more if it goes unnoticed). Try to check the md5 sums generated…
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Depends on the output your are getting, say its something like below, saved in a dataframe `df` that countains your `FoldEnrichment` values…
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Might also be worth looking at the CELLxGENE database and selecting Visium datasets. The corresponding publication may provide the addition…
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Not for that but to know the % of CNV inherited in order to know the sensitivity of the caller
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This is really helpful and beyond what I've expected. Thank you
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Thank you, I already extracted manually, as I am using WSL, and directories are correct, and I still get the error saying "Segmentation fa…
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Thx. I found out that I used the wrong reference genome. I have a set of data from mice and a set from humans. I processed the human data u…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
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Thx. It turns out that the file was damaged during transmission.
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Depending on how much of that information is personally identifiable you may not be able to get the metadata unless you get approval from d…
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