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Search took 0.00 seconds. Search: Posts Made By: yu_chem
Forum: Bioinformatics 08-25-2020, 09:26 AM
Replies: 0
Views: 913
Posted By yu_chem
About samples of RNA-seq in Ensembl database for primate and etc

Thank you for reading.
I would like to know the samples of RNA-seq in Ensembl.

At present, I want to analyze RNA-seq data from primate (e.g. Chimpanzee) to new world monkey (e.g. Marmoset)....
Forum: Bioinformatics 07-27-2018, 03:59 AM
Replies: 0
Views: 877
Posted By yu_chem
A package to fit multivariate Gaussian mixture model

Hello.
I ask you about R package or others
Now I have expression data of some genes from 10x genomics

I want to get multivariate Gaussian mixture model fitted to data for showing relationship...
Forum: Bioinformatics 05-25-2018, 11:10 AM
Replies: 0
Views: 1,016
Posted By yu_chem
what statistical test is better to compare two distributions

Dear SEQ members

I'd like to ask you about the test for distribution.
I hope you give me information of test for similarity of two distribution

Now I have two distribution data contains...
Forum: Bioinformatics 04-15-2018, 11:01 AM
Replies: 1
Views: 924
Posted By yu_chem
How to analysis WGBS data

Hello

I'm analyzing WGBS (bulk) data from ENCODE project.
I would like to know how do many researchers analyze WGBS data.

When I extracted CpG sites having > 10 coverage on 20 samples, CpG...
Forum: Bioinformatics 04-10-2018, 10:47 AM
Replies: 0
Views: 675
Posted By yu_chem
How to use SVA for removing noise from WGBS data

Hello
I'm analyzing WGBS methylome data (tissue sample) and I would like to remove noise (batch effect and blood contamination).
I read some papers about reference-free deconvolution for removing...
Forum: Bioinformatics 11-27-2017, 01:27 AM
Replies: 0
Views: 1,098
Posted By yu_chem
How to name lncRNA and miRNA

Hello everyone

I would like to ask you about how to name lncRNA and miRNA.
Following paper suggests that the part of lncRNA were named by homology (FAM class, TTTY class, and so) and position...
Forum: Bioinformatics 05-20-2017, 06:56 AM
Replies: 6
Views: 2,638
Posted By yu_chem
Dear mastal I really appreciate your sincere...

Dear mastal

I really appreciate your sincere response for my question.
Forum: Bioinformatics 05-20-2017, 02:45 AM
Replies: 6
Views: 2,638
Posted By yu_chem
Dear mastal Thank you for answer. I...

Dear mastal

Thank you for answer.
I checked , for genes on the minus strand, the exon closest to the rightmost end ((B) column in below expamle) of the gene is labelled as exon_number 1 (like...
Forum: Bioinformatics 05-19-2017, 08:42 AM
Replies: 6
Views: 2,638
Posted By yu_chem
Dear mastal Thank you for your answer and...

Dear mastal

Thank you for your answer and sorry my basic question.
Do you mean that as transcription mechanism (from below site), when strand of certain gene is decided, the side close to TSS is...
Forum: Bioinformatics 05-19-2017, 06:09 AM
Replies: 6
Views: 2,638
Posted By yu_chem
How to decide the side (5' or 3') close to TSS in GTF

Hi everybody

I’d like to ask you about TSS (transcription start site) annotation
Now I’m analyzing Total RNA-seq data by ENCODE project.
I will check reported relationship between gene...
Forum: Bioinformatics 03-11-2017, 08:35 AM
Replies: 0
Views: 1,672
Posted By yu_chem
Smile Reconstruction method of repeatMasker output

Hi everyone

I'd like to ask you about reconstruction method of repeatMasker output.
These days, I started my new research project about ERV.
Now I'm using repeatMasker and Repbase latest version...
Forum: Bioinformatics 11-05-2016, 08:33 AM
Replies: 4
Views: 2,068
Posted By yu_chem
Thank you for answer. I understood. I'll look...

Thank you for answer.
I understood. I'll look up more information based on the above.
Forum: Bioinformatics 11-03-2016, 09:42 AM
Replies: 4
Views: 2,068
Posted By yu_chem
Thank you for answer I understood about Entrez...

Thank you for answer
I understood about Entrez ID and checked gene_info

If possible, I hope you answer following question.
Is Entrez gene symbol official gene symbol provided by HGNC and MGI?
...
Forum: Bioinformatics 10-31-2016, 06:46 PM
Replies: 4
Views: 2,068
Posted By yu_chem
Gene identifier provided by NCBI

Hi everyone

I ask you about gene identifier.
I know that NCBI provide several gene identifier e.g. Entrez gene symbol, Entrez gene ID, Unigene, Official gene and so, but I don't know proper use...
Forum: Bioinformatics 10-29-2016, 07:17 PM
Replies: 4
Views: 2,469
Posted By yu_chem
Thank you for answer. Aren't all Entrez genes ymbol the same as symbol of HGNC ?

Thank you for answer. Aren't all Entrez genes symbol the same symbol of
HGNC ?
Although I can judge a kind of ID (e.g. NM_*** ENSG ***), I don't know how to judge a kind of symbol (e.g. Entrez...
Forum: Bioinformatics 10-29-2016, 06:53 AM
Replies: 4
Views: 2,469
Posted By yu_chem
Thank you for answer. Is 5460 entrez gene ID and not symbol ?

Thank you for answer. I understood that POU5F1 is provided by HGNC (checked this page https://www.ncbi.nlm.nih.gov/gene/5460). I'll check refFlat and GTF tomorrow.
you told me that 5460 is entrez...
Forum: Bioinformatics 10-28-2016, 06:59 AM
Replies: 4
Views: 2,469
Posted By yu_chem
What kind of Gene symbol do annotation files (refFlat and GTF) contain ?

Hi everyone

I would like to ask you about the kind of gene symbol which refFlat and GTF file contain.
I downloaded human genome reference (hg19) and associated files from iGenome and I'm going to...
Forum: Bioinformatics 01-30-2016, 06:00 AM
Replies: 0
Views: 1,608
Posted By yu_chem
E-value of MEME

Hello everyone,

Could you tell me about the calculation formula of E-value?
I could not find the calculation formula for E-value of MEME-ChIP (motif-based sequence analysis tools).
I checked the...
Forum: Bioinformatics 06-18-2015, 03:41 AM
Replies: 2
Views: 1,853
Posted By yu_chem
Thank you for answer. Sorry that I have not...

Thank you for answer.
Sorry that I have not studied enough.

On the basis of your hint, I will study more
Forum: Bioinformatics 06-15-2015, 10:10 AM
Replies: 2
Views: 1,853
Posted By yu_chem
How to give peaks data of ChIP-seq annotation

Hi everyone

I want to ask you how to give peaks data of ChIP-seq annotation.
For understanding peaks data generated by MACS as bed file or xls file of peaks, I want to know What genes including...
Forum: Bioinformatics 03-06-2015, 02:49 AM
Replies: 4
Views: 3,169
Posted By yu_chem
Dear Genomax Thank you for answer and I'm...

Dear Genomax

Thank you for answer and I'm sorry for delay of the reply.
I also try using other database.
It's reason for selecting these files of genome and genes that when I started to learn...
Forum: Bioinformatics 03-06-2015, 02:25 AM
Replies: 4
Views: 3,169
Posted By yu_chem
Dear Richard Finney. Thank you for answer...

Dear Richard Finney.

Thank you for answer and I' sorry about delay of the reply
After I commanded formatdb, blast creates files: database-name.nsq, database-name.nhr and database-name.nin and...
Forum: Bioinformatics 03-03-2015, 07:56 AM
Replies: 4
Views: 3,169
Posted By yu_chem
How to install local blast on linux

Hi everybody

Now I’m bothered with setting of local blast-2.2.26 on linux
Please help me. I'm beginner as bioinfomatician.

I have downloaded local blast-2.2.26, homo_sapiens genome and Refseq...
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