steve odette
I am a Para-vet- BSc. Animal health and production with passion for good veterinary practices.
Location Kenya
Activity
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steve odette made a comment
I am currently developing a course that I will deliver online. I could have targeted a face-to-face audience but the logistics plus my target reach do not align.
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steve odette made a comment
In terms of target audience, size of the audience, learning outcomes, and content/topics, I see no significant difference in terms of quality. All three formats perform pretty well. However, when it comes to assessment, face-to-face and virtual formats perform pretty well-- The fact that assessments here involve project work brings a big difference compared to...
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steve odette made a comment
I choose 2. And maybe this resonates much with my experience being a student and how I like to approach teaching. As the instructor, it is incumbent upon me to be the originator of information. There is a reason why I am the instructor and people want to learn from me. May be I have experience in that domain or have mastered something that should be relayed...
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steve odette made a comment
Experiences where all learners are engaged can be rare. In my life time, at least they are rare. However, I was watching one lecture by Professor Denis Nobel, and I must admit, that was really thought out. I was in my full concentration. So I can imagine those who were in that lecture. The secrete to this lecture was making sure content is well researched,...
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steve odette made a comment
I hope for
more on data analysis across diverse samples -
steve odette made a comment
Glad I finished the course.
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steve odette made a comment
EX1:
var_tb %>% ggplot(aes(y=DP, x=ALT_DP)) + geom_point()
ex2:
var_tb %>% ggplot(aes(y=DP, x=ALT_DP, fill = SAMPLE)) + geom_point(shape = 21, size = 5) + scale_fill_brewer(palette = "RdBu")
ex3:
test <- var_tb %>% ggplot(aes(y=DP, x=ALT_DP, fill = SAMPLE)) + geom_point(shape = 21, size = 5) +
scale_fill_brewer(palette = "RdBu") +
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steve odette made a comment
Impressive. Especially the analysis of genes parts
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steve odette made a comment
EX1:
variants_csv2 |> group_by(SAMPLE) |> summarise(mean(DP))
Ex2:
variants_csv2 |> group_by(SAMPLE) |> count(CHROM, sort = TRUE) |> head(6)
Ex3:
var_tb %>% mutate(DP100 = DP/100) %>% select(SAMPLE, DP, DP100) %>% str() -
steve odette made a comment
Another alternative to %>% is base R's |>.
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steve odette made a comment
This week's learning is good for general data exploration. Allows you to have a feel of your data. Also, the learnings allows you prepare/subset only the data you want to use in future.
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steve odette made a comment
My significant learning point is assigning lineages.
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I found this helpful:
"Ir may be because your home directory is full. There should be a ~/.singularity directory there that could be filling up. Can you try and delete that and try again?"
Comment edited from the nextflow guys -
steve odette made a comment
This worked for me just as it is:
nextflow run nf-core/viralrecon -profile singularity \
--max_memory '12.GB' --max_cpus 4 \
--input samplesheet.csv \
--outdir results/viralrecon \
--protocol amplicon \
--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 3 \
--skip_kraken2 \
--skip_assembly \
--skip_pangolin \
--skip_nextclade... -
steve odette made a comment
bcftools stats gives me this:
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 76
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 75
SN 0 number of MNPs: 0
SN 0 number of indels: 1
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0 -
steve odette made a comment
I would begin with the basics, Watson and Crick's discoveries of the structure of the DNA, I mean how can you sequence what you do not know about? Top of my list is also PCR by Kary Mullis. Most NGS technologies use fundamentals of PCR. Then now I can come to sanger sequencing.
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steve odette made a comment
I am Steve Odette, from Kenya. I have some basic bioinformatics skills but want to scale up.
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steve odette made a comment
Hi, I have installed everything right. Can someone help me with this error?
"samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory" -
steve odette replied to steve odette
@UchennaUrom Hi, yea your code is right. I should not have used the "==" but "eq". #iterate Ephania's resp.
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steve odette replied to Laura Carrillo
Working with wnds. This worked before running R
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steve odette made a comment
I was not able to start R in git using the "R" command. Command not found
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steve odette made a comment
read -p "Enter the filename:" File
function file_exists () {
if [[ -e ${File} ]]
then
echo "File exists": ${File}
else
echo "The File ${File} does not exist"
fi
}
file_exists "${File}" -
steve odette made a comment
for (( i=1; i<=5; i++))
do
if [[ ${1} == 2 ]]
then
echo "fizz"
else
echo "buzz"
fi
done -
steve odette made a comment
read -p "Please enter a diamond cut: " quality
if [[ ${quality} == "Fair" ]] || [[ ${quality} == "Good" ]]
then
echo "Insufficient quality to proceed"
elif [[ ${quality} != "Ideal" ]] && [[ ${quality} != "Very Good" ]] && [[ ${quality} != "Premium"
]]
then
# If the cut is not a valid value
echo "Invalid cut"
else
# Using the -c option from grep... -
steve odette made a comment
echo "What sound does the animal give"
read animal
case $animal in
cow)
echo "Here, moo"
;;
sheep)
echo "there a baa"
;;
duck)
echo "Everywhere a quack"
;;
*)
echo "Old MacDonald had a farm"
esac -
steve odette made a comment
echo "what your the temperature"
read temperature
min_temp=10
max_temp=30
if [[ ${temperature} -gt ${max_temp} ]]
then
echo too hot
elif [[ ${temperature} -lt ${min_temp} ]]
then
echo too cold
elif [[ ${temperature} -gt ${min_temp} ]] && [[ ${temperature} -lt ${max_temp} ]]
then
echo just okay
fi -
steve odette made a comment
fruits=("pineapple" "peach" "raspberry" "plum" "apple" "kiwi")
echo "we have ${#fruits[@]} elements"
echo "last fruit is ${fruits[-1]}"
