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Recent Replies

Answer: How to understand Hisat2 aligment result
by
rbj
•
0

Or alternatively this example with Hisat2 is also useful
[here][1]
[1]: https://www.biostars.org/p/313264/

Comment: BLAST options error: File homo_ref.faa does not exist
by
logbio
▴
30

When I try what you said and run the makeblast command again, this time I get the following error. "`BLAST options error: homo_ref.faa does…

Comment: scatterplot in R
by
bioinformatics
▴
10

Ok thanks for your response. If the sd and mean values are not part of the table where should I put them?
I'm hoping to end up with 2 erro…

Comment: scatterplot in R
by
Asaf
9.3k

Each row is one sample so the mean and sd should not be a part of the table. There are elegant ways to plot the mean and SD of a population…

Comment: scatterplot in R
by
bioinformatics
▴
10

Ok thanks. I have ended up with a mean value and sd for each population.
Is this table correct?
head(df)
Samples Expressi…

Comment: scatterplot in R
by
Asaf
9.3k

Compute it using all the expression values in the population (samples in each tumor type I assume). You will end up with one value for each…

Comment: antismash error
by
kblin
▴
30

Hi there, sorry for the late reply. I don't seem to get notification emails here on Biostars.
You'd run your FASTA file like:
```
anti…

Comment: scatterplot in R
by
bioinformatics
▴
10

Ok thanks for your help. How might I correctly calculate the SD?

Comment: scatterplot in R
by
Asaf
9.3k

You're misusing this formula. STDEV.S is for estimating the standard deviation of a population. What you are computing is basically the dis…

Answer: antismash download databases issue.
by
kblin
▴
30

The script should install the databases into the database directory. By default, this is in your antiSMASH install location. You can howeve…

Comment: scatterplot in R
by
bioinformatics
▴
10

The sd of an individual point is how spread the point/expression value of the gene in the sample is from the mean expression of all the sam…

Comment: scatterplot in R
by
Asaf
9.3k

What is the meaning of `sd` for an individual point? SD is relevant when considering a population. You can compute the mean and SD of the p…

Comment: scatterplot in R
by
bioinformatics
▴
10

In response to this comment:
You got a bit of a mess here. First of all you switched the parameters Samples and Expression.value, Samples …

Comment: scatterplot in R
by
Asaf
9.3k

You got a bit of a mess here. First of all you switched the parameters Samples and Expression.value, Samples should be on the X (first para…

Comment: scatterplot in R
by
bioinformatics
▴
10

I have used this command:
TIMP1Plot <- ggplot(df, aes(Expression.value, Samples, colour = Tumour.type)) + geom_point() + geom_errorbar…

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