Very informative videos! Love you videos. Can you please make a video on differential gene expression analysis from TCGA using R.
@AKBIT
2 жыл бұрын
Sure. I'll post soon.
@iommoh5869
4 жыл бұрын
Thank you Ashok
@AKBIT
4 жыл бұрын
You're welcome!
@meditationrelaxingpeaceful5632
Жыл бұрын
Sir In ncbi forms to get the accession number, there is column for reference author. What to write there?
@AKBIT
Жыл бұрын
Reference author means the 'name' of the data submitter.
@meditationrelaxingpeaceful5632
Жыл бұрын
@@AKBIT thanks sir! What to write in? FORWARD PRIMER NAME REVERSE PRIMER NAME Sequence Author Isolation source Isolation place
@AKBIT
Жыл бұрын
Can you mention the timeline in the video where you have doubt?
@debashrutidas2974
2 жыл бұрын
Thank You. But it would be better if you either say or write the instruction in the video
@AKBIT
2 жыл бұрын
Thank you for your feedback. I will follow in future video making.
@waqarali4721
3 жыл бұрын
How to get the P-vale and logFC value for dataset from GEO also how to identify the differential expressed gene ?
@AKBIT
3 жыл бұрын
Use GEO2R site www.ncbi.nlm.nih.gov/geo/geo2r/
@nastaranmarzban1419
2 жыл бұрын
Hi, hope you're doing well My major is statistics and unfortunately i know almost nothing about genetics... But i have to do some analyses on them. I have two questions, would you please help me? 1) We have 100 people, for each of them we measure their genotypes. I wanna know that are these genes have features? If i want to explain about what i mean by features, i should say that for example for each atom , say oxygen, we have specific number of protons, electrons and .... but among chemical which has oxygen, there are different number of oxygen... So features means something that is fix. Now I wanna know that do we have features for each gene?(something that is fixed and not change for different people, genotypes are changed among different people) 2) if the answer of above question is yes(we have genotypes for each pesron,they are changing from one person to another, and we have features for each genes), how can i have data like this? I'll be very thankful if you help me... Thanks in advance.
@AKBIT
2 жыл бұрын
Genetics is a vast area to explain. According to your query, I'll explain simply. All living organisms have feature. In physical aspect, you can consider body parts/organs which are common - but varies like tall, short, fat, etc. In biological aspect, genetic memory, genetic disorders, etc. - but varies over evolution due to genetic crossover (father & mother).
@zuraizbutt6592
3 жыл бұрын
Select a raw data set of Arabidopsis thaliana from GEO. Put it into GALAXY and de-contaminate it. After filtering you are supposed to align it on the any of the prescribed reference and show the results Tell me plz how i do
@AKBIT
3 жыл бұрын
Your question is not clear to understand.
@aishwaryas4696
Жыл бұрын
Sir, could you add voice explanation for this video. I'm an undergrad. I find it difficult to understand what's going on
@AKBIT
Жыл бұрын
Sorry for the inconvenience. In future videos the problem will be rectified. If you have any queries, send mail to ashok.bioinformatics@gmail.com
@Jan20052005
4 жыл бұрын
Why you select the lower value in in Sample Rank ?
@AKBIT
4 жыл бұрын
Lower rank represents higher accuracy. Rank is similar to grading system.
@VijayaLakshmi-jq1mz
3 жыл бұрын
from GSE68465 I want to delete GSMXXXX samples which are related to dead patients and normal patients. How do I delete. Can you help me in solving this query for my research.
@AKBIT
3 жыл бұрын
You cannot delete or modify datasets stored in the database. If you want to ignore GSMXXXX samples which are related to dead patients and normal patients, you must select samples (CTRL + Left click the hits for multiple selection) and assign group name(s). Now, you can analyze the selected samples (group) alone. For brief explanation, watch this video kzitem.info/news/bejne/pouG03uNjGqanmU
@virgirma1328_PhD_scholar
2 жыл бұрын
Hello sir!How to contact you please?
@AKBIT
2 жыл бұрын
ashok.bioinformatics@gmail.com
@Sophie-hb8ht
4 жыл бұрын
What software/app do you use to download soft files?
@AKBIT
4 жыл бұрын
You can directly download using browser itself.
@backtesting12
3 жыл бұрын
@@AKBIT i cant download file ,
@AKBIT
3 жыл бұрын
@@backtesting12 0:55 Watch at this timeline to download the dataset. NCBI have temporarily restricted to download some datasets through FTP. It may possibly be removed from the NCBI server.
@namratajawanjal9549
3 жыл бұрын
Hello Sir, Thank you for sharing this video. Very useful. I am working a little bit sane concept. Up to this, I understood how to download the RNA-Seq dataset using NCBI-GEO. But after this how-to align this data? I have to differentiate between a common splicing site and an alternative splicing site. Please suggest me.
@AKBIT
3 жыл бұрын
Sorry for the late response. GEO2R is the build-in gene expression data analysis (based on R language) tool. I'll post a video on it soon. www.ncbi.nlm.nih.gov/geo/geo2r/
@namratajawanjal9549
3 жыл бұрын
@@AKBIT Sir, I have one query on how I can differentiate between a common splicing site and an alternative splicing site. Which data from NCBI do I have to use Transcript data of a particular gene or any other data? After that, I have to align that data. Please suggest me.
@AKBIT
3 жыл бұрын
@@namratajawanjal9549 You can download a common splicing site or alternative splicing site from NCBI-GEO, but it must be relevant to your research. The NCBI-GEO supports data analysis through GEO2R with a specific dataset or profiles only. Aligning the RNA-seq dataset can be done through many software. Galaxy is a commonly used cloud server that consists of many alignment tools for RNA-seq data analysis.
@AKBIT
3 жыл бұрын
@@namratajawanjal9549 Refer this article it will be useful to you www.ncbi.nlm.nih.gov/pmc/articles/PMC5476949/
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