Ruth Nanjala
Ruth is a bioinformatician who’s previously led the Bioinformatics Mentorship and Incubation program at icipe, Kenya. She is also a Carpentries instructor.
Location United Kingdom
Activity
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When mapping, you have to index with "bwa index" before running "bwa mem". Samtools indexing assists with visualization on IGV.
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We changed the question
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@VictorHugoMuñozMora you might want to check whether it is available on your system. Run "module avail", copy the freebayes code and paste it on the command line. For example: "module load freebayes/1.3.1"
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This means the file is missing, probably the alignment step did not run successfully? or you are in the wrong folder?
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Probably restart the virtual machine.
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Yes they can.
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What Operating system are you using? Did you install Miniconda? Did you download the yml file?
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Ruth Nanjala replied to Gabriel Abah
The process is similar, what changes is the command.
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Hard clipping:
As opposed to soft clipping, hard clipping permanently removes entire sequence segments or bases.
Consider the following scenario: you have Illumina paired-end reads, and the adaptor sequences utilized during library preparation were left in the sequencing data. These adapter sequences at the ends of the reads have been identified as...
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@CeciliaLai @SuffianAzizan @AlexandruBologa
Soft clipping:
Here, parts of a sequence, typically read alignments, are marked as potentially unreliable but are not entirely removed. Instead, they are considered in the analysis, but with the understanding that they might contain errors or variations.Assume you have a lengthy DNA sequence that was read...
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Ruth Nanjala replied to Mariene Amorim
Yes it should, although you also use "porechop", "pycoQC","NanoPlot" and so on...
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Ensure you downloaded the yml file and created an environment using the yml file.
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The exercises, starting from quality control
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@MERCILENABENJAMIN try running "fastq-dump --help", If it gives you a help page then it was installed successfully.
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It is paired-end data
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Apologies for that, was an oversight. Should be 2 statements which have now been edited.
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@VictorHugoMuñozMora if you go to to the "Variant Calling" step, it is explained in detail
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Ruth Nanjala replied to Iliya Ndams
Download the yml file, create conda environment, activate it then start running the commands
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Try this:
wget https://www.futurelearn.com/links/f/9shs5409fm00sshumwoz2jijpxedtm7
then:
unzip MOOC.yml.zip
then:
conda env create -n MOOC --file MOOC.yml
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Try installing using Homebrew
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If you run the command:
wget https://www.futurelearn.com/links/f/9shs5409fm00sshumwoz2jijpxedtm7
then:
unzip MOOC.yml.zip
then:
conda env create -n MOOC --file MOOC.yml
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Try installing with Homebrew
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You can use either
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If you run the command:
wget https://www.futurelearn.com/links/f/9shs5409fm00sshumwoz2jijpxedtm7
then:
unzip MOOC.yml.zip
then:
conda env create -n MOOC --file MOOC.yml
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Try installing using Homebrew
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If you run the command:
wget https://www.futurelearn.com/links/f/9shs5409fm00sshumwoz2jijpxedtm7
then:
unzip MOOC.yml.zip
then:
conda env create -n MOOC --file MOOC.yml
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@MERCILENABENJAMIN no, you should be good.
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Run the command on the folder where your downloaded file is.
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You should run the command in the folder containing the downloaded file.
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If the conda works fine, you don't need to uninstall it. Work on creating the conda environment MOOC, and activate it.
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Ruth Nanjala replied to Valeria Chiluiza
It is always advisable to work with the latest versions of tools/softwares although any Linux version should be okay.
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You are right, we have edited the question. Apologies for the oversight.
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@SampathNarayanan
This could be as a result of different things:1. operating system (Ensure you are on Linux or MacOS that is not M1 or M2)
2. check that the code is written correctly i.e no spaces that shouldn't be there
3. Update conda
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This could be as a result of different things:
1. operating system (Ensure you are on Linux or MacOS that is not M1 or M2)
2. check that the code is written correctly i.e no spaces that shouldn't be there
3. Update conda -
Or install the VirtualBox
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If you installed using conda, "conda list" will list all the tools, otherwise call each tool on the command line.
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Bioconda is a channel in conda. Please install miniconda to get all channels.
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@KenSaville you need to activate the conda environment before calling the tools. Did you run "conda activate MOOC"?
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Could you please elaborate?
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Ruth Nanjala replied to Fredua Agyeman Bawua
1.7 Setup for this course. Look at the link shared close to the end of the page. @jyotsanasingh @ForbesKanyumbwe
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Install Windows Subsystem for Linux. Instructions are attached within the course materials.
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Docker is a container.
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What Operating system are you using?
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Ruth Nanjala replied to Thiloka Ratnaike
If you are using a mac, conda should work if its not M1 or M2, otherwise use Homebrew to install the tools @ThilokaRatnaike.
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Ruth Nanjala replied to Fredua Agyeman Bawua
Please use Windows Subsystem for Linux. Link attached to the course.
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No, the MOOC environment should be used on Linux or MacOS that does not have the M1 or M2 chip. If you have a MacOS with M1 or M2 chip, install the tools using Homebrew.
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Please download Windows Subsystem for Linux first. Link is attached on the course description
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In FASTQ files, quality scores are commonly calculated using the Phred scale. The Phred score is a logarithmic measure of the probability that a base (nucleotide) in a DNA sequence is called incorrectly. It is expressed as a quality score (Q) and is calculated using the formula:
Q = -10 * log10(P)
Where:
Q is the Phred quality score.
P is the... -
Ruth Nanjala replied to Osuchukwu Uchenna
Windows subsystem for Linux. The link to the tutorial has been attached to the course.
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which operating system are you using?
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Ruth Nanjala replied to Mwangi Denis
Index it again using "samtools faidx MN908947.fasta"
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