Understanding File Formats in Bioinformatics: ChIP-Seq files - BigWig (Wiggle) and BED/bigBed

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  • เผยแพร่เมื่อ 9 ก.ย. 2024

ความคิดเห็น • 18

  • @hansikapatel2843
    @hansikapatel2843 2 วันที่ผ่านมา

    Very nice speech ❤❤👍👌

  • @shantanujain3732
    @shantanujain3732 ปีที่แล้ว

    This was a great explanation. Thank you :)

  • @varshatripathi9857
    @varshatripathi9857 ปีที่แล้ว +1

    Plz make a vedio of Pathway enrichment analysis through Cluster profiler package...

  • @lailanhass1988
    @lailanhass1988 6 หลายเดือนก่อน

    Thanks!

  • @abdelrahmanmahany133
    @abdelrahmanmahany133 7 หลายเดือนก่อน

    Thanks for the great effort. Can you recommend the sequence to watch your playlists so that it would be in the right order? Thanks again

  • @mervanbayraktar5269
    @mervanbayraktar5269 ปีที่แล้ว

    Thank you so much for the work that you’re doing, can you please make video about genome wide association study and genetic diversity and population structure best regards

  • @user-rk4tl7xx2i
    @user-rk4tl7xx2i 11 หลายเดือนก่อน

    Hi. very infomative video.
    Could you do a video about Methylation NGS data treatment if you are familiar with it ?
    Thanks a lot !

  • @shajibdey6451
    @shajibdey6451 ปีที่แล้ว

    Hi. Informative video indeed.
    If I have some hypothetical proteins of a bacteria, will I be able to get it's gene ID?
    please let me know. Thanks in advance.

  • @Po0pypoopy
    @Po0pypoopy ปีที่แล้ว +1

    I’m not sure if you have made a video on this already but :
    Can you make a video about how to get into bioinformatics ?
    I quit my job as a wet lab assistant from a research lab 2.5 years ago and haven’t done anything related to biology since then because I was very upset with the income and lack of learning opportunities, I have zero letters of recommendations now because I quit when my boss and colleague didn’t want me to because they really needed me even though I was upset. I currently just have a bachelors.
    I’m having a very hard time figuring out how to get into this field with no letters of recommendations
    Would trying to make a personal project be enough? Should I join clinical research trials and learn some biostatistics?
    I feel like nobody would want me if I can’t get any letters of recommendation 😢
    Lost and need help….thanks

    • @localsofindia1457
      @localsofindia1457 6 หลายเดือนก่อน

      may i know what u are doing now?

    • @Po0pypoopy
      @Po0pypoopy 6 หลายเดือนก่อน

      @@localsofindia1457 nothing….i have given up on life

    • @Po0pypoopy
      @Po0pypoopy 6 หลายเดือนก่อน

      @@localsofindia1457 nothing since I gave up on life

  • @florianm5639
    @florianm5639 ปีที่แล้ว

    Great video! Very clarifying! I have a further question. How does one deal with repetitive regions such as the rDNA locus? In my dataset I see the highest read count at the rDNA but for some reason it is not called as a significant peak. Do you have any idea on how to deal with this? Thanks:)

    • @Bioinformagician
      @Bioinformagician  ปีที่แล้ว

      A common approach for dealing with repetitive regions is to mask or filter out these regions. ENCODE provides a list of such blacklisted regions. In your case, it seems the outcome is favorable. You should not expect to see a significant peak in your repetitive region (in most cases). Repetitive regions may appear enriched by looking at the number of reads mapping to that region, hence it is important that the ChIP-Seq profile is compared to a matched input control to determine its significance.

    • @florianm5639
      @florianm5639 ปีที่แล้ว

      @@Bioinformagician Actually, that would not be favorable, as I am working on such a region. But maybe the method then is just not suited? In any case. Thanks for the reply!

    • @Bioinformagician
      @Bioinformagician  ปีที่แล้ว

      Thank you for clarifying it. Sorry, I misunderstood your query initially. Determining significant peaks in repetitive regions can be challenging. One way you could improve the detection of peaks in these regions, is by lowering the p/q value threshold while calling peaks (for programs like MACS), however be wary of lots of noise and false positive peaks that you will be getting in your results. Another rudimentary way that I can think to determine significant peak enrichment, is to calculate the number of reads mapping to these regions in your sample and matched normal and calculating fold change. The fold change would give you a good indication for enrichment in that region. Lastly, I recommend referring to a published study that have studied chromatin modifications and transcription factor binding to rDNA as there could be orthogonal methods/assays which I am not aware of, that you can use to add confidence to your findings by the methods mentioned above.

    • @florianm5639
      @florianm5639 ปีที่แล้ว

      @@Bioinformagician Sounds like a good place to start! Thank you!