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Recent Replies
Comment: RNASEQ differential expression of paired samples
by
hans
•
0
Thank you,
The tutorial seems to provide the right solution
Comment: problem with no replicate data analysis
by
Bioinformatics1
•
0
it is my pleasure to communicate with you.
Do you have an example of no replicate data for RNA seq analysis to share with me? RNA seq lab …
Comment: Error in plot-vcfstats
by
samuelandjw
▴
80
Install the absent file. See https://pkgs.org/download/tex(memoir.cls)
Comment: Using vcftools and got Error: Unknown option: --max-missing
by
samuelandjw
▴
80
Try bcftools instead. The author of vcftools has ceased updating vcftools for a while.
Answer: [Biopython] endweight, endopen and endextend equivalent for Bio.Align.PairwiseAl
by
Mensur Dlakic
★
12k
Have you tried adding:
aligner.end_open_gap_score = -10
aligner.end_extend_gap_score = -1
Comment: plot-vcfstats
by
samuelandjw
▴
80
Please see my edited answer. If my answer helps you, please consider accepting it.
Comment: how to filter out all the homozygous genotypes in a multi sample VCF file?
by
Nahid Bandi K
•
0
Thank you zengjingyu and @sbstevenlee for your help and explanations. I guess as @sbstevenlee explained if I remove all the homozygous geno…
Comment: Help with Volcano plot
by
Kevin Blighe
76k
Please use *KEGGprofile* (I just posted an answer here: https://support.bioconductor.org/p/9138854/), or some other pathway analysis progra…
Comment: UMI counts and read counts in GeneGlobe output
by
Abhishek
•
0
Thank you for the confirmation.
Would there be any reason the READs columns are provided too ?
I'm thinking maybe for normalizing the UMI…
Comment: problem with no replicate data analysis
by
Gordon Smyth
★
2.9k
Actually I wrote page 24 of the edgeR User's Guide, but I can't give you customized advice specific to your dataset. If you know nothing at…
Comment: problem with no replicate data analysis
by
Bioinformatics1
•
0
Gordon, What do I add instead of the housekeeping index? I only have data, I don't know how to add the housekeeping gene. Please read page …
Answer: problem with no replicate data analysis
by
Gordon Smyth
★
2.9k
The edgeR User's Guide (to which you link) has an entire section called "What to do if you have no replicates". That section enumerates all…
Comment: Help with Volcano plot
by
mshubham
•
0
How can I annotate the pathways associated with the genes labeled above?
Since they are very small set of genes, I only want to annotate t…
Answer: UMI counts and read counts in GeneGlobe output
by
i.sudbery
12k
Your understanding is correct. The reads are the counts of all reads mapping to a given gene. UMIs is the number of distinct UMIs, and ther…
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