Wow! I have no words to describe how thankful I am for this tutorial. I'm at the beggining of my Master Degree and although it may seem simple to someone, trying to solve this problem for my project took me a week. Thank you SO much, you're brilliant!
Fantastic channel! I've been trying to go through dozens of different tutorials on transcriptomic data and was getting quite lost. Your tutorials summarise a lot of knowledge into clear and straightforward steps. Thank you very much!
Thank you so much -- I learned so much more from this than reading the documentation on Bioconductor. Watching you use the web version first helped me understand the code in R better.
Interesting tutorial! I was trying to merge Human Cell Atlas (HCA) with Mouse CA from Immgen. Following this, I wanted to annotate the clusters for cell types. This video helps me know the Ensembl ID > gene signatures. Cheers! Thanks.
Hi. thanks a lot for the great content. I really appreciate if you answer my question. is it possible that I get the results in the same order that I provide the ENSMBLEs? because I wanted to convert thousands of Ensembles to gene symbols and the I realized that the results are not in the same order. I have done DESEQ2 and at the end need to get the names of significant genes with all the other infos together. thanks again
Do you have a video explaning how to convert gene IDs across species? I am mostly intersted in converting genes from non-model species (Fathead Minnow fish for example) to either human or mouse or zebrafish IDs. Thanks so MUCH!!!!!
Very Nice mam...I have one doubt, in my research I have list of SNP id near about 50000 and its reference sequence assembly available on NCBI. Now I want to find that how much from this SNP anotated with functional gene. How can I do ?....plz explain mam
There is a plant ensembl as well, which you can use. If you still don't find your species in there, you can download .gff file (genomevolution.org/GenomeInfo.pl?gid=32935) associated with the species and retrieve information from it. Given you have protein sequences another option is to use uniprot. You can programmatically access it and retrieve IDs associated with your protein sequences. Check this article out: www.ncbi.nlm.nih.gov/pmc/articles/PMC6275023/ It points to some useful resources.
You are a wonderful teacher! Though I watch your video for the first time. I have some gene id, these gene id aren't ensembl id, to be honest, I don't know these gene id's variety, I need change them to symbol id. In the past, I always used the microarray platform to convert gene id, I just need to input GPL number, but this time, the microarray is a new one, nearly all the R packages haven't indexed it. The annotation of the GPL in GEO database only provide base sequences and unfamiliar gene id. I want to know how can I get those convert to symbol id? Thanks! Please forgive my poor English.😂
thankyou, also i have one question that how can we extract the output obtained.i.e., the table of gene_id and their symbols in excel sheet/format please suggest.
How do you deal with the same conversion from ensembl transcript IDs? Sometimes, I get multiple duplicate genes. Is there a way to filter duplicates out?
If it's the counts data I am dealing with, I would first filter out the genes with low counts and then map my ensembl IDs to the gene symbol. If the goal is to perform differential expression analysis, I would first run the analysis with ensembl gene IDs and then convert the IDs to symbols for downstream steps. Lastly if I have a table of normalized counts (FPKM or TPM), I take the row means and keep the row with max mean (This could be a little risky as means are affected by outlier values).
M'am for ensemble ids with version number, which keytype to match? I tried with entrezid but its reducing the rows and for anailable rows many symbol names are NA
Choose 'rat genes' dataset in bioMart to gene mappings to rat genome. Similarly, you will also find 'org.Rn.eg.db' i.e. rat equivalent of 'org.Hs.eg.db' and 'EnsDb.Rnorvegicus.v79' of 'EnsDb.Hsapiens.v86'
Hi! Thanks for this useful tutorial. How can I get a gene list from multiple values (or, more specifically a .bed file with chromosome, start site, and end site for a number of CpGs)?
Hi! Thanks for these videos, they are super useful! I have a question about converting gene IDs in an anndata file. I need to convert the ensembl IDs to gene symbols- the anndata file I'm working with has gene IDs set as the index..and this makes it tricky..any suggestions? Thanks again
Hi Surya, I think you mean Ensembl ids have version numbers. For instance ENSG00000227232.4. Because of these version numbers(after the dot), gene names are not retrieved from the database and it gets tricky. So to remove these version numbers either you can do it in an excel sheet using Find and Replace command or you can use this command in R #Remove version numbers from gene ids IDS
@@shilpisehgal5613 Hi! thanks for your reply I have removed the dots from the ENSEMBL IDs- that's not the issue. I'm trying to reset the index of my anndata file with another column with all the matching gene names, while also removing the NAs? Does that make sense?
Thank you so much for this tutorial and it helps me retrieve my gene symbol! However, I have 60k gene id I would like to convert it to gene symbol and it only can convert 500 gene id at max, how can I convert the rest of it?
Wow! I have no words to describe how thankful I am for this tutorial. I'm at the beggining of my Master Degree and although it may seem simple to someone, trying to solve this problem for my project took me a week. Thank you SO much, you're brilliant!
Fantastic channel! I've been trying to go through dozens of different tutorials on transcriptomic data and was getting quite lost. Your tutorials summarise a lot of knowledge into clear and straightforward steps. Thank you very much!
Thank you so much -- I learned so much more from this than reading the documentation on Bioconductor. Watching you use the web version first helped me understand the code in R better.
Interesting tutorial! I was trying to merge Human Cell Atlas (HCA) with Mouse CA from Immgen. Following this, I wanted to annotate the clusters for cell types. This video helps me know the Ensembl ID > gene signatures. Cheers! Thanks.
The best Bioinformatics Teacher.
Hi. thanks a lot for the great content. I really appreciate if you answer my question. is it possible that I get the results in the same order that I provide the ENSMBLEs? because I wanted to convert thousands of Ensembles to gene symbols and the I realized that the results are not in the same order. I have done DESEQ2 and at the end need to get the names of significant genes with all the other infos together. thanks again
Many thanks for sharing a new wonderful tutorial. Eager to see the next one!
Do you have a video explaning how to convert gene IDs across species? I am mostly intersted in converting genes from non-model species (Fathead Minnow fish for example) to either human or mouse or zebrafish IDs. Thanks so MUCH!!!!!
Thanks a lot, very helpful. Webtool and R methods 2 & 3 are straightforward. Method 1 (biomart on R) is not intuitive.
Hi dear what you present is good but would be more interesting if you do methylation analysis. Also about variant calling etc
Thanks for the suggestion. I'll surely plan on making a video covering these topics.
Hi Ae We, please do check out my bioinformatics RUclips channel for more insights: ruclips.net/channel/UCNhVAcIdarXzTCWZ27N1EmQ on variants, etc.
Very Nice mam...I have one doubt, in my research I have list of SNP id near about 50000 and its reference sequence assembly available on NCBI. Now I want to find that how much from this SNP anotated with functional gene. How can I do ?....plz explain mam
Thanks a million for this fantastic videos. Keep going powerfully
annotables pacakge is not avialable in the recent version of R as well as in cran and bioconductor
Thank you! what happens if there is no one-to-one mapping between geneids and genesymbols, how to proceed then?
It could be possible that the ID corresponds to a non protein-coding gene.
Hi. I found the tutorial very useful. Just one query, is it possible to get Gene names close to our intergenic variants ensemble ids?
Thank you again for this video. And, I am studying with plant materials so would you tell me which package I can do annotation for plant species?;
Thanks a ton for sharing this! I was wondering if I want to convert the gene ID in Seurat object how it works?
Mam no information of cicer arietenum in ensemble then what can be the other way to get gene sequences and their I'd if i have protein sequences.
There is a plant ensembl as well, which you can use. If you still don't find your species in there, you can download .gff file (genomevolution.org/GenomeInfo.pl?gid=32935) associated with the species and retrieve information from it.
Given you have protein sequences another option is to use uniprot. You can programmatically access it and retrieve IDs associated with your protein sequences.
Check this article out: www.ncbi.nlm.nih.gov/pmc/articles/PMC6275023/ It points to some useful resources.
Thanks mam I will try
You are a wonderful teacher! Though I watch your video for the first time. I have some gene id, these gene id aren't ensembl id, to be honest, I don't know these gene id's variety, I need change them to symbol id. In the past, I always used the microarray platform to convert gene id, I just need to input GPL number, but this time, the microarray is a new one, nearly all the R packages haven't indexed it. The annotation of the GPL in GEO database only provide base sequences and unfamiliar gene id. I want to know how can I get those convert to symbol id? Thanks! Please forgive my poor English.😂
I tried all methods, and all the time I am getting more than from my own gene list, and a lot of NA, what can be the reason
Thank you for this video !!
Thanks
thankyou, also i have one question that how can we extract the output obtained.i.e., the table of gene_id and their symbols in excel sheet/format please suggest.
You can use write.table() to export your file as a csv/tsv and then open it into excel.
@@Bioinformagician thankyou
M'am How to save this output to system?
It can just be redirected to a data.frame. For example:
output.mappings
How do you deal with the same conversion from ensembl transcript IDs? Sometimes, I get multiple duplicate genes. Is there a way to filter duplicates out?
If it's the counts data I am dealing with, I would first filter out the genes with low counts and then map my ensembl IDs to the gene symbol. If the goal is to perform differential expression analysis, I would first run the analysis with ensembl gene IDs and then convert the IDs to symbols for downstream steps.
Lastly if I have a table of normalized counts (FPKM or TPM), I take the row means and keep the row with max mean (This could be a little risky as means are affected by outlier values).
@@Bioinformagician thank you
M'am for ensemble ids with version number, which keytype to match? I tried with entrezid but its reducing the rows and for anailable rows many symbol names are NA
Those could be non-coding mRNAs and hence you get NAs for those entrez IDs.
I think you should try removing the version numbers.
I really like you videos! Thank you! What to do for the rat transcriptome?
Choose 'rat genes' dataset in bioMart to gene mappings to rat genome. Similarly, you will also find 'org.Rn.eg.db' i.e. rat equivalent of 'org.Hs.eg.db' and 'EnsDb.Rnorvegicus.v79' of 'EnsDb.Hsapiens.v86'
Hi! Thanks for this useful tutorial. How can I get a gene list from multiple values (or, more specifically a .bed file with chromosome, start site, and end site for a number of CpGs)?
HiNice video. Is it possible to explain the pam50 classification of breast cancer by probe id conversion? Thank you so much.
Hi! Thanks for these videos, they are super useful!
I have a question about converting gene IDs in an anndata file.
I need to convert the ensembl IDs to gene symbols- the anndata file I'm working with has gene IDs set as the index..and this makes it tricky..any suggestions?
Thanks again
I am not sure if I understand "set as the index" means. Can you please elaborate?
Hi Surya, I think you mean Ensembl ids have version numbers. For instance ENSG00000227232.4. Because of these version numbers(after the dot), gene names are not retrieved from the database and it gets tricky. So to remove these version numbers either you can do it in an excel sheet using Find and Replace command or you can use this command in R
#Remove version numbers from gene ids
IDS
@@shilpisehgal5613 Hi! thanks for your reply
I have removed the dots from the ENSEMBL IDs- that's not the issue.
I'm trying to reset the index of my anndata file with another column with all the matching gene names, while also removing the NAs?
Does that make sense?
you saved me 🙂
M'am Can we do the same procedure for all genome builds?
Most packages would support GRCh37 and GRCh38. I am not sure about the earlier builds, will have to check that.
@@Bioinformagician Thankyou
Thank you so much for this tutorial and it helps me retrieve my gene symbol! However, I have 60k gene id I would like to convert it to gene symbol and it only can convert 500 gene id at max, how can I convert the rest of it?
Are these ensembl gene IDs? Also, are you using biomart? Do you mind sharing the code snippet you are running?
When I tried second method- I get this error
Error: object 'grch38' not found
Did you load annotables R library before running it?