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Recent Replies
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK
by
chrchang523
9.3k
During VCF (or .bgen) import, something needs to be done to convert the input single-part IDs to PLINK's two-part IDs. `--const-fid 0` is …
Comment: User error in GATK CreateSomaticPanelOfNormals
by
Hasib
•
0
Hi, sorry for the late reply. I ended up not creating a PoN from my own normal sample and downloaded necessary PoN and reference genome fil…
Comment: all coding regions .bed file hg38 Whole Genome Sequencing
by
Pierre Lindenbaum
146k
unrelated to the original question.
Comment: Incomplete alignment EMBOSS needleall
by
bioinformatics.queries
▴
50
Thank you so much for your response. A simple tweak from fastq to fasta solved the problem and global alignment was turned off :-). Cheers.…
Comment: all coding regions .bed file hg38 Whole Genome Sequencing
by
hdjc90
•
0
Thank you for this. Can I ask, what is the best method to filter/extract only variants that appear in the exome (i.e. in the generated .bed…
Answer: How to compare two sequence logo?
by
Mensur Dlakic
★
19k
We don't know whether you are talking about protein or DNA/RNA motifs, so my answer will be general.
If you are talking about finding mo…
Comment: How can I find DEGs between groups in one cluster of scRNA-Seq Seurat object?
by
Zahra
▴
50
@cpad0112
Thanks for your reply. I have tried to perform the Pseudobulk method but my Seurat object doesn't have any information about th…
Comment: How to compare two sequence logo?
by
GenoMax
117k
> should I align them together
If you want to compare then you will need at least two things to do so. So finding motifs separately would …
Comment: Finding common pattern among heterogenous group of cancer
by
Matthias Zepper
▴
920
It is just a quirk of mine, but I sometimes applied tools to data that were actually meant for a different purpose, if the inputs were sort…
Comment: RNA-seq pipeline for degraded RNA
by
yussab
▴
70
thank you very much for your feedback, I really appreciate it. Unfortunatelly I have more degradaded (as precious) RNAs. DegNorm seems to w…
Comment: Align short sequence against ONT reads
by
andres.firrincieli
★
2.5k
ONT reads can have a lot of errors and if the exon is to short the following solution might not work for the noisy reads.
Use shred.sh fro…
Comment: How to compare two sequence logo?
by
rpolicastro
8.8k
Can you expand on your question more? It's unclear what data you have and what you want to do with it.
Comment: Finding a known duplication mutation in a VCF file
by
Pierre Lindenbaum
146k
> The VCF is the only input file I got.
so the only tool I know is `bcftools roh` but IMHO, you cannot check if there is a true positive w…
Comment: Finding a known duplication mutation in a VCF file
by
langzvi
•
0
It's a gene with length of 35,548 nt according to NCBI, so it's pretty big. So, you suggest converting the VCF to a BAM file?
The VCF is th…
Comment: Searching for RNA-seq melanoma samples in TCGA or cBioPortal
by
JACKY
▴
10
I want processed SKCM data (preferably counts, but normalized data would also work.. like RPKM or TPM). And for the same samples, I want t…
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