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Recent Replies
Comment: DESeq2: How do I evaluate PCA before and after setting covariates in design matr
by
sr41489
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0
Thanks again for your help, and my apologies again for asking these basic questions (I'm very new to this and don't have a formal education…
Answer: Adding an extra/dummy chromosome to reference genome
by
Pierre Lindenbaum
147k
cat ref.fa plasmid.fa > newref.fa
samtools faidx newref.fa
samtools dict newref.fa > newref.dict
Answer: Genome-wide enrichment of histone marks and correlation with gene expression: Ap
by
LChart
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320
Short answer: I haven't managed to find any libraries for performing this kind of analysis end-to-end. Given that the input is multi-variat…
Comment: How to produce count matrix with multiple run files?
by
Antonio R. Franco
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4.9k
I don't see the point of mixing different samples when you are running a single-cell experiment. I've been reading the tutorial, and ended …
Comment: Converting bedgraph file to wig file
by
ATpoint
64k
x-posted https://support.bioconductor.org/p/9145939/ Please indicate crossposts across communities.
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
Ok what ever this command line is it seems to be working. Kill this job and then copy this command into your job submission script.
Comment: What are GL*.* values in chr column of rna seq counts?
by
GenoMax
118k
That was the case with previous genome assembly `hg19` when this was a valid accession. Since that time this sequence likely made it into m…
Comment: Using Harmony on scATAC Count Files
by
bioinformatics.girl
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0
No. I am asking how to merge 2 fragment files *before starting an ArchR project.
Comment: How to know the genome indices from STAR is correct
by
Chris
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0
Aug 09 12:43:41 ..... started STAR run
Aug 09 12:43:41 ..... loading genome
Aug 09 12:45:05 ..... started mapping
Answer: Using Harmony on scATAC Count Files
by
LChart
▴
320
`ArchR` has built-in support for Harmony correction;
```
projHeme2 <- addHarmony(
ArchRProj = projHeme2,
reducedDims = "Iter…
Comment: Splitting Gbff files
by
Istvan Albert
94k
The code is really simple. The parsing step reads the original multi-genbank file, then the loop writes into a filename that uses the recor…
Comment: What are GL*.* values in chr column of rna seq counts?
by
syntax
▴
60
thank you. hmm, so they found evidence that this sequence exists but do not yet know where it resides in the genome?
Answer: What are GL*.* values in chr column of rna seq counts?
by
GenoMax
118k
Those are unlocalized genomic contigs. Here is one example of an example record that is now deprecated: https://www.ncbi.nlm.nih.gov/nuccor…
Comment: How to know the genome indices from STAR is correct
by
GenoMax
118k
Did you try running the STAR command directly on the terminal prompt as I suggested above?
Answer: Help with adding variables to PCA
by
swbarnes2
12k
My guess is splitting up the males and females is introducing errors. I'd guess the problem is that you are using a subset of pc_dif for t…
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