Thank you!! I am from other field, and interested at bioinformatics. However, I feel it is difficult to find a hands-on tutorial to follow... Thank you for your sharing!!
Many thanks for sharing the video, but my problem is the same as you faced, in experiment design or do not know exactly, because I also cannot get the required significantly up and down regulated genes, could you please share a video to solve this problem? or do you have any before, if yes, could you please share the link here?
Thank you as always for the good information. Just to clarify the usage of DESeq2- what's the difference between using contrasts in the result function, and specifying this information in the design argument to the deseqdatafrommatrix function? (i.e., I have 2 relevant non-dependant variables- the treatment, and the tissue from which the sample was taken. should I specify them in contrasts, or in the design argument when building the deseq object?)
Hi, we have put together a list of videos to watch accordingly if you want to conduct a rna-seq step by step (www.liquidbrain.org/videos) do check it and see if it helps :)
Oh i just realized you many copy number not count number, not sure I am late to the party, but perhaps you can try this www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/cnv_analysis.html
Sorry, its Rsubread not Rsubgene, I have corrected those in the slides (as attached in the video description)
@LiquidBrain I would suggest that you pin this comment so that it appears at the top
your channel is now my new "tv show" addiction...lol....keep all these analyses coming...
Really good video- please keep them coming. Would love a series on DNA/RNA sequencing and analysis!
Thank you!! I am from other field, and interested at bioinformatics. However, I feel it is difficult to find a hands-on tutorial to follow... Thank you for your sharing!!
The argument annot.ext =- ann does not work for me in the function featureCounts. And this is the type of error i get:
fc_SE
Wonderful walkthrough!
you are life saver, seriously!!
Thank you very much for the video.
Thanks a lot, very nice and clear talk!!!
Thank you so much for your nice explanation
Thank you for making the video
I am very new to RNA sequencing, how is the input file a reads.txt.gz? and not fastq files? what am I missing in between?
Do I need to use a super computer for this? Or a desktop with 12GB RAM can also be used?
Yes it doesn’t consume much computing power, yours is more than good enough . -Lind
@@LiquidBrain thank you for your reply.
Many thanks for sharing the video, but my problem is the same as you faced, in experiment design or do not know exactly, because I also cannot get the required significantly up and down regulated genes, could you please share a video to solve this problem? or do you have any before, if yes, could you please share the link here?
Thank you as always for the good information. Just to clarify the usage of DESeq2- what's the difference between using contrasts in the result function, and specifying this information in the design argument to the deseqdatafrommatrix function? (i.e., I have 2 relevant non-dependant variables- the treatment, and the tissue from which the sample was taken. should I specify them in contrasts, or in the design argument when building the deseq object?)
One question: this is after fastqc right?
I want to analyse the next generation sequencing data analysis.For that reason what I should do.
Hi, we have put together a list of videos to watch accordingly if you want to conduct a rna-seq step by step
(www.liquidbrain.org/videos) do check it and see if it helps :)
Would love to see a video on obtaining copy number profiles from NGS data (processed bam files) - I have not found a good video in that!
Try featurescount in galaxy 😬so far the easiest way to get a count matrix from a bam file if you are able to annotate them some other way
@@LiquidBrain thanks!
I don’t have any experience using galaxy. I am trying to use Gatk but not having much luck :)
Oh i just realized you many copy number not count number, not sure I am late to the party, but perhaps you can try this
www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/cnv_analysis.html
Thank you
Great job!