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Answer: featureCounts segmentation fault
Answer: featureCounts segmentation fault
Comment: Cloud storage option for uploading Bioconductor Annotation package
Comment: Pedigree information
Answer: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
Answer: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
A: What is the difference between GRCh37 and hs37? And hg19?
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Recent Replies
Answer: HTseq count issue, not aligning to features
by
MolGeek
▴ 80
Have you checked if the cromosome names are represented the same way in both bam files and the gtf/gff? For example if in bams the chromoso…
Comment: Cloud storage option for uploading Bioconductor Annotation package
by
KABILAN
▴ 80
Okay.. for getting quick response I posted in both platforms...
Comment: featureCounts segmentation fault
by
Darked89
4.7k
`featureCounts` will also accept bgzip-ed and tabix indexed `GTF`. It may be a bit faster than using plain `GTF` but frankly I have not don…
Answer: Sankey + dot plot
by
dthorbur
★ 2.4k
Here is a rough outline you can start to play with using the dataset you provided. It creates separate Sankey and dot plots, but you can cr…
Comment: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
by
Ian
6.1k
Thank you I did not realise I could do that.
Comment: RNA-Seq mutation calling without germline data
by
Shred
★ 1.5k
Sorry for the delay. These are (legit, not stupid!) questions related to the usage, so would be better to do not flood the answer section o…
Comment: How to convert CSV format to VCF using Python?
by
Darked89
4.7k
You do not have enough columns to transform your `CSV` into `VCF` ver 4.2. There are just `CHROM POS ID REF ALT` end even that is being gen…
Comment: Cloud storage option for uploading Bioconductor Annotation package
by
GenoMax
146k
> I contacted hubs@bioconductor.org three days ago regarding SAS tokens. Perhaps you just need to be patient. Looks like you already post…
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
▴ 250
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
▴ 250
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…
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