User: luzglongoria
luzglongoria • 20
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- 6 months, 1 week ago
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Posts by luzglongoria
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... Sorry, I didn't say. It is RNA-seq ...
written 8 hours ago by
luzglongoria • 20
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... hi there,
I need to do some statistical analyses of my transcriptomes.
I have a database with 4 columns (gene ID (categoric), expression level (numeric), individual, species). I have 2 different species and 5 ind per species. Per each individual I have more than 20000 genes (some of them are more ...
written 8 hours ago by
luzglongoria • 20
• updated
6 hours ago by
ATpoint ♦ 14k
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... Solved!
It was a problem with the title of the first column :) ...
written 4 days ago by
luzglongoria • 20
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... Hi,
I am trying to create a heatmap.
Before I need to transform my dataset:
data <- heatmap_data
rnames <- data[,1] # assign labels in column 1 to "rnames"
mat_data <- data.matrix(data[,2:ncol(data)]) # transform columns (I have) into a matrix
...
written 4 days ago by
luzglongoria • 20
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... Hi,
I am trying to create a heatmap by using ggplot but when I try to indicate the min and max values of my data, R automatically modifes the values.
I show you what I have done:
My data:
![original data][1]
Showing 1 to 14 of 22 entries
library(ggplot2)
library(reshape2)
## transf ...
written 4 days ago by
luzglongoria • 20
• updated
4 days ago by
Friederike ♦ 3.2k
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Comment:
A: How to run Trinotate
... Thank you so much h.mon for your answer.
However, I get an error message when I try to run the command for Trinotate.
I have create a conf.txt file that looks like:
# progs
TRANSDECODER_DIR=/home/luz_garcia_longoria/miniconda3/pkgs/transdecoder-5.5.0-0
BLASTX_PROG=/home/luz_garcia_lo ...
written 19 days ago by
luzglongoria • 20
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Comment:
C: How to run Trinotate
... Thank you so much for your answer. I will try like this :) ...
written 19 days ago by
luzglongoria • 20
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... Hi,
I need to use Trinotate for finishing my transcriptomic analyses. I have followed the instructions in :
https://github.com/Trinotate/Trinotate.github.io/wiki
I am in the step called ' Automated Execution of Trinotate: Running computes and loading results' . Apart from running Trinotate itself ...
written 19 days ago by
luzglongoria • 20
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Comment:
C: Basic question about SWISSPROT
... Thanks.
What I want is to search against SWISSPROT using the Trinity.fasta file.
The problem is that I am working with a spp. from Plasmodium which genome is not anywhere. So, I am not sure whether I need to download a subset of proteins from SWISSPROT (by selecting all the ones from Plasmodium i ...
written 4 weeks ago by
luzglongoria • 20
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Comment:
C: Basic question about SWISSPROT
... Ok, I see. But then, how can I create my own database of interesting sequenced?
Thanks ...
written 4 weeks ago by
luzglongoria • 20
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