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Recent Replies
Answer: how to make box plot of specific row with group of sample in R
by
rpolicastro
5.8k
Here is some example data.
# Counts table.
counts <- as.data.frame(replicate(4, sample(1:100, 6)))
colnames(counts) <- spr…
Comment: How can I get PHRED score?
by
Riku
▴
30
Sorry for not responding sooner.
Thanks to you, I was able to get PHRED score with multiqc.
It was very easy to just run multiqc in the di…
Comment: Primers and multimapping ?
by
ATpoint
53k
If you want to design primers properly in this regard use PrimerBLAST which extends Primer3 by BLASTing hits against a genome to avoid exac…
Comment: Primers and multimapping ?
by
Pierre Lindenbaum
138k
unrelated to bioninformatics. You'll get any PCR product if any of the multiple location of the foward is close to the revere on the same …
Comment: How can I get PHRED score?
by
Riku
▴
30
Thank you very much for your advices!
It seems that I have to check fastq file.
Comment: Ensembl vep singularity
by
ATpoint
53k
Can you try to run it as `singularity exec --no-home --cleanenv`?
Comment: Can't locate Bio/SeqIO.pm - path error?
by
blur
▴
200
I tried that too - I opened the env where snippy is installed and ran
conda install -c bioconda perl-bioperl
I get a msg: "All reque…
Comment: Can’t run trinity - Java version
by
biofalconch
▴
480
A little bit difficult without a little bit more context, but I think you have to specify the path, but also don't forget the quotations! ,…
Comment: What is the cutoff used for define high or low expression level of gene for surv
by
txtbookir
▴
10
Dear kevin, i have used median cutoff via the code below, but for quantile how can i change the code?
median_value = median(clin_df$ge…
Comment: Loading a genome in BSgenome
by
josev.die
▴
50
Hi.
You are right. We followed that vignette to forge our custom genomes :
- [chickpea][1]
- [asparagus][2]
[1]: https://www.bioco…
Comment: Use BLAST Command Line Applications to run a folder of many sequences against a
by
a.zielezinski
9.8k
Is there any chance you could share FASTA files of query and individual species?
Comment: DESeq2 errors for RNA-SEQ data analysis in R studio
by
ATpoint
53k
Move the gene column of the count data to rownames first so the count table only contains the counts as columns.
Comment: 23andme file format
by
Ahmadreza
•
0
What if the variant is a deletion or insertion, particularly of more than a nucleotide? How could you differentiate an insertion of -/TT fr…
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