RNASeq Analysis | Differential Expressed Genes (DEGs) from FastQ

[@liquidbrainr7081]

Sorry, its Rsubread not Rsubgene, I have corrected those in the slides (as attached in the video description)

[@muungani]

@LiquidBrain I would suggest that you pin this comment so that it appears at the top

[@davidotohinoyi3082]

your channel is now my new "tv show" addiction...lol....keep all these analyses coming...

[@imi9894]

Really good video- please keep them coming. Would love a series on DNA/RNA sequencing and analysis!

[@YYHo-kw2bi]

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!!

[@marasmanucleare5747]

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

[@ehteshamulislam4640]

Is it not necessary to trim the adapters and deduplicate rhe reads before alignment?

[@akshaybareja4697]

Wonderful walkthrough!

[@sumithra1324]

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?

[@lamjennygrace623]

you are life saver, seriously!!

[@pingliu1310]

Thanks a lot, very nice and clear talk!!!

[@maryamsediqi3726]

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?

[@TheTomerm]

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?)

[@johirislam8174]

I want to analyse the next generation sequencing data analysis.For that reason what I should do.

[@LiquidBrain]

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 :)

[@MrRamaeri]

Thank you so much for your nice explanation

[@JenniFadoni]

Thank you very much for the video.

[@davidguardamino]

One question: this is after fastqc right?

[@nghieply7951]

Thank you for making the video

[@norsolehamohddali3273]

Do I need to use a super computer for this? Or a desktop with 12GB RAM can also be used?

[@LiquidBrain]

Yes it doesn’t consume much computing power, yours is more than good enough . -Lind

[@norsolehamohddali3273]

@@LiquidBrain thank you for your reply.

[@imi9894]

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!

[@LiquidBrain]

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

[@imi9894]

@@LiquidBrain thanks! I don’t have any experience using galaxy. I am trying to use Gatk but not having much luck :)

[@LiquidBrain]

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

[@大黑能]

Thank you

[@Saed7630]

Great job!