Mahendra Singh

Mahendra  Singh

I have a master in Big data analytics
and Bioinformatics from JNU New Delhi, India and here I'm signing up to understand, explore, and upgrade the new concepts

Location New Delhi

Achievements

Activity

  • Task:1
    Navigate the Unix command line to perform basic data manipulation tasks relevant to NGS analysis.

    Analyze RNA-Seq and CHiP-seq data to identify relevant biological insights (e.g., differential gene expression, protein binding sites).

  • Setting clear expectations for group work in learning environments. It suggests strategies like ground rules or co-created codes of conduct to ensure all members contribute effectively.

    The value of group facilitation: The instructor is encouraged to engage with each group individually, checking understanding, answering questions, and offering guidance...

  • To sum up, group work allows learners to:
    1. Learn from each other (peer learning)
    2. Tackle real-world problems and develop practical skills
    3. Engage actively with the topic through discussions and application

    However, facilitating effective group learning requires specific skills, as facilitators guide learners and create an environment for...

  • Key Points:
    1. Understanding Audiences
    2. Delivering training material and collaborating with domain experts
    3. Sharing data and conducting project-based training

  • Happy to learn from the experts

  • Hello Everyone, My name is Mahendra from India and I have a master's major in Bioinformatics and Data Science, currently working as a bioinformatician in a research Lab here at the Univerisity of Delhi.

    Super Excited, to join this course to learn how to train trainees about genomics and bioinformatics.

    Thank you,

  • Hey @DzmitryDauhalevich thanks for reporting, maybe I can fix this later on. well in my case all the images are open.

  • Hey, @RiddhimaKhatri do you have all the FastQ files along with fastq_dir_to_samplesheet.py file. in the same folder? if this is correct please run the command in the same folder or check each step again, in my case it works well.

  • Hi Everyone, I have created a week three practice notebook on GitHub for each step here is the link below: Please open it on the Firefox web browser and start practicing in one go..

    https://github.com/Mahendra687/BioiAnalysing-and-Interpreting-Genomics-Datasets/blob/main/Week3/Week3.ipynb

    Thank you, Happy Learning :)

  • Hi Everyone, I have created a week two practice notebook on GitHub for each step here is the link below: Please open it on the Firefox web browser and start practicing in one go..

    https://github.com/Mahendra687/BioiAnalysing-and-Interpreting-Genomics-Datasets/blob/main/Week2/week2.ipynb

    Thank you, Happy Learning :)

  • Thank you :)

  • I look forward to learning all aspects of RNA Seq Data Analysis

    Thank you WCS Team :)

  • @AndriesvanTonder Hi, I am getting an error when I run the following command: (base) ms@Extensa:~/dataset/data$ ./nextflow run nf-core/viralrecon -profile singularity \
    --max_memory '12.GB' --max_cpus 4 \
    --input samplesheet.csv \
    --outdir results/viralrecon \
    --protocol amplicon \
    --genome 'MN908947' \
    --primer_set artic \
    --primer_set_version 3...

  • Getting the following error:

    ERROR ~ To perform variant calling in amplicon mode please provide a valid primer BED file e.g. '--primer_bed primers.bed'.
    -- Check '.nextflow.log' file for details

    can anyone discuss this with me? about this

  • @OkenlaQahhar Hey, I am getting the same error did you solve this?

  • Hey, did you fix it? I got the same error:

    hey @Fayik Suhail I did this the following way: steps are below

    https://github.com/Mahendra687/BioiAnalysing-and-Interpreting-Genomics-Datasets/blob/main/Week2/week2.ipynb

  • after running your code I get the "fastq_dir_to_samplesheet.py" on my data directory next I run the second command: $ python3 fastq_dir_to_samplesheet.py data samplesheet.csv -r1 _1.fastq.gz -r2 _2.fastq.gz
    which end up with the following error:
    "NameError: name 'false' is not defined. Did you mean: 'False'?

    How do we fix this, did you get the same error?...

  • Thanks

  • Is anyone able to download Python script file from the above link if yes then please share it with me at mahendras948@gmail.com

    Thank you

  • Hey, are u able to open the following link: https://raw.githubusercontent.com/nf-core/viralrecon/master/bin/fastq_dir_to_samplesheet.py to download the Python script

    please let me know if you have python script file that we are trying to download but unfortunately not please mail me at: mahendras948@gmail.com

  • Hi, you need to ensure that the directory exists. before running the command if the directory does not exist then you can create it as well for example, I have created a directory for this course by the following command: $ mkdir ~/MOOC

    Now, move the nextflow executable command: $ mv next flow ~/MOOC/

  • The take-home line: In the workflow, the output of one tool/package becomes the input of the next tool/package.

  • welcome :)

  • @OlukayodeObisanya, @KomalZia happy to hear that :)

  • For me, Nextflow and Snakemake are on top of the WfMS and looking to understand parallel processing by applying WfMS approaches.

  • Hi Everyone, I have created a week one practice notebook on GitHub for each step here is the link below: Please open it on the Firefox browser and start practicing in one go..

    https://github.com/Mahendra687/BioiAnalysing-and-Interpreting-Genomics-Datasets/blob/main/Week1/wee.ipynb

    Thank you, Happy Learning :)

  • Hi Everyone, I have created a week one practice notebook on GitHub for each step here is the link below: Please open it on the Firefox browser and start practicing in one go..

    https://github.com/Mahendra687/BioiAnalysing-and-Interpreting-Genomics-Datasets/blob/main/Week1/wee.ipynb

    Thank you, Happy Learning :)

  • I got the same result INDEL: 1 + SNPs: 75 total = 76

  • Here are the General Statistics: from MultiQC which is very close to FastQC

    Sample Name
    ERR5743893_1:% Dups: 95.3% | % GC: 39% | Median Read Length: 221 bp M Seqs: 0.2

    ERR5743893_2:% Dups: 94.1% | % GC: 39% | Median Read Length: 201 bp M Seqs: 0.2

  • The main difference between a SAM file and a BAM file is its format. SAM files are plain text and human-readable, while BAM files are binary and more compact, making them better suited for storage and computational efficiency.

    SAM files are uncompressed, which means they can be larger and take up more disk space compared to BAM files.
    BAM files are...

  • Mahendra Singh made a comment

    DNA Structure, Polymerase, and Sanger Seq

  • Hey Everyone, I am looking for research-based NGS data analysis and am open to any collaborative work if anyone is interested let me know.

    Thank you,

  • @FarkhandaMahmood Hey I want to have a discussion with you too

  • To sum up, NGS Tech came up with:
    Accuracy
    Higher coverage,
    Enhanced precision, and
    Greater sequence reliability.

    the advantages of time, cost, sample size, and accuracy make NGS an applicable tool in medical settings and genomic research.

  • INSIGHTFUL

  • interesting

  • looking forward to this

  • Page was not found for Artificial Intelligence: How to get it right

  • Mahendra Singh made a comment

    I enjoyed a lot about data

  • agree

  • Challenge: is converting the Unstructured data into Structured data

  • Data: unstructured data
    Formats: image
    Challenges: Finding the fractures using ML

  • Challenges: the major challenge is Cleaning, preparing and analysing the data
    Benefits: AI and Machine Learning able to address the healthcare problems

  • tabular form

  • Workflow:
    Preprocess the Datasets----> Create or split the train and test datasets -----> Build the model-----> Evaluate and Refine the model----- Come up with the conclusion

  • Mahendra Singh made a comment

    Thank you!

  • This is very informative.

  • 1. Random Forest is the supervised learning and
    2. Neural Network is the unsupervised learning

  • AI can be able to solve complex problems by understanding the data.

  • Alright, so we are going to transform the health-related problem by applying the AI

  • Great!__good to know you all

  • Hi everyone, I'm mahendra from India and I have a master in big data and bioinformatics from JNU, New Delhi and currently looking for PhD position. here I'm joining this course to learn as much as I can about Genomics and Bioinformatics to express myself in front of the audience.

    Thank you,

  • Installation is done!

  • Very informative slide ____some typo error need to correct

    Thank you,

  • Yeah, Feature Engineering is an important part of ML algorithms implementation.

  • Really excited, to start a new journey with AI and Bioinformatics

  • Perfect!

  • > x = c(3,10,30)
    > x
    [1] 3 10 30

    > m = rep(x, times = 2)
    > m
    [1] 3 10 30 3 10 30

    > n = c(x, 0, x)
    > n
    [1] 3 10 30 0 3 10 30

    > m == n
    [1] TRUE TRUE TRUE FALSE FALSE FALSE FALSE

    > length(m)
    [1] 7

    > length(n)
    [1] 7

  • All done!

  • me too!

  • Mahendra Singh made a comment

    #!/usr/bin/env bash
    for (( i=1; i<=5; i++ ))
    do
    if [[ $i -eq 2 ]]
    then
    echo "DNA"

    else
    echo "RNA"

    fi

    done

    Output:
    RNA
    DNA
    RNA
    RNA
    RNA

  • #!/usr/bin/env bash
    animal=$1
    case $animal in
    cow)
    echo "Here a moo"
    ;;
    sheep)
    echo "There a baa"
    ;;
    duck)
    echo "Everywhere a quack quack"
    ;;
    *)
    echo "Old MacD had a farm"
    ;;
    esac

    Run: ./farm.sh duck
    Output: Everywhere a quack quack

  • @VictoriaOfford, Thank you

  • Just right!

  • Mahendra Singh made a comment

    #!/usr/bin/env bash

    #array for fruits
    fruits=("pineapple" "peach" "raspberry" "plum" "apple" "kiwi")
    #Number of element in the array
    echo "Number of fruits: ${#fruits[@]}"
    #Last element in the array
    echo "Last name of the fruits: ${fruits[5]}"

    Output:
    Number of fruits: 6
    Last name of the fruits: kiwi

    An alternative way:
    #!/usr/bin/env...

  • Two way to run bash scripts:
    Relative path: ./myscript.sh
    Absolute Path: ~/myscript.sh

  • @SergioCohecha Thank you! I thought it will fix by a command.

  • Welcome!@LuísTeves

  • I have (base) indicator too, is there any problem with this..?

  • Good Morning!

    When I run: $nano hello.sh shebang path does not appear in the nano editor what should I do..? to appear.
    @Victoria Offord @Fellow_Learner

  • interesting!

  • excited to learn bash scripts

  • you can do the same as I did here:
    /Desktop/FT/Data/Week1_Data$ cd ..
    /Desktop/FT/Data$ cd ..
    /Desktop/FT$ cd ..
    /Desktop$ cd ..
    @mahendra:~$

    from Week1_Data to home directory

  • Me too

  • @AlassaneditBaneyeMaiga cd space .. for example, cd .. to come back home or parent directory!

  • @LuísTeves you can also use rmdir command to remove directory

  • move the course_data into working Directory using mv command!

  • Ans:1
    Week1_Data$ grep -F difference *.*
    ghandi_2.txt:The difference between what we do
    ghandi_cut.txt:The difference
    ghandi.txt:The difference between what we do
    ghandi.txt.out:The difference

    Ans:2
    Week1_Data$ grep -Fc Premium Diamonds_fix.txt
    13791

    Ans:3
    Week1_Data$ grep -Fcv "Very Good" Diamonds_fix.txt
    41859

    is that correct..?

  • nano DNA.txt
    cat DNA.txt
    AGCT
    GCTA
    TACG
    AGCT
    TCAG
    GCAT
    CAGT
    AGTC
    ATTT
    TTTA
    GAGT
    sort DNA.txt | uniq -id
    AGCT
    sort DNA.txt | uniq -id | uniq -i > repeated_DNA.txt
    cat repeated_DNA.txt
    AGCT

  • QC is the part of Data Pre-Processing before the analysis Data should be cleaned to analyzed meaningfully

  • After running the command: tail -2 Diamonds.csv
    only one line displayed...why?
    But in case of command: head -2 Diamonds.csv
    two lines displayed

  • me too

  • Hi, @Marcos
    less: It displays the contents of a file one page at a time and navigates both forward and backward through the file.

  • After running this command: Week1_Data$ sort < Diamonds_fix.txt | less
    How do we come back to the current directory is there any command to back..?

  • @MartinAslett Thank you

  • Yeah, interesting

  • can be move directory to the next instead of files?

  • I familiar with a few interesting new commands:
    ls -lt
    ls -ltr
    man -ls and
    info

    Thank you, Martin

  • @RodneyRees Thank you,

  • Alright!

  • correct

  • I already installed Ubuntu and it's very handy to work on biological data.

  • Done

  • Nice to meet you!

  • Hi,
    I am Mahendra from India, a Master student and want to learn Linux with R to apply in Biological Data Analysis.

    Thank You,

  • Meaningful story.