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Recent Votes
A: Chip-seq best practice data analysis
Answer: featureCounts segmentation fault
Answer: Benchmark hg19 vcf by hs37d5 vcf
Answer: Benchmark hg19 vcf by hs37d5 vcf
Comment: RNA-Seq mutation calling without germline data
Answer: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
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Recent Replies
Comment: featureCounts segmentation fault
by
ATpoint
84k
Please show relevant code. This is almost certainly some issue with the GTF.
Comment: Are tens of DEGs still biologically meaningful?
by
DGTool
▴ 230
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…
Answer: When to use integration with scRNASeq
by
ATpoint
84k
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 …
Comment: DESEQ with time series data on mutant vs. wild-type?
by
ATpoint
84k
Yes, this interaction term would capture genes where the difference between day and night is altered as a consequence of genotype. Note tho…
Comment: featureCounts segmentation fault
by
DGTool
▴ 230
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…
Answer: LOC gene on opposite DNA-strand causes lower log2FC value?
by
ATpoint
84k
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…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Michael
55k
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…
Comment: Visualizing Upregulated and Downregulated Genes in GO and KEGG Pathway Analyses
by
Nat.Nataren
▴ 90
Depends on the output your are getting, say its something like below, saved in a dataframe `df` that countains your `FoldEnrichment` values…
Comment: how to get visium HD dataset with its information
by
Nat.Nataren
▴ 90
Might also be worth looking at the CELLxGENE database and selecting Visium datasets. The corresponding publication may provide the addition…
Comment: Mendelian precison
by
heureuse
• 0
Not for that but to know the % of CNV inherited in order to know the sensitivity of the caller
Comment: Mendelian precison
by
heureuse
• 0
This is really helpful and beyond what I've expected. Thank you
Comment: featureCounts segmentation fault
by
Jaber
• 0
Thank you, I already extracted manually, as I am using WSL, and directories are correct, and I still get the error saying "Segmentation fa…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
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.
by
Pallondyle
• 0
Thx. It turns out that the file was damaged during transmission.
Comment: how to get visium HD dataset with its information
by
GenoMax
145k
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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