User: Whoknows

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Whoknows650
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Tehran,Iran
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Posts by Whoknows

<prev • 145 results • page 1 of 15 • next >
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Answer: A: DNA sequence of genes from vcf file
... Hi You could create a table consists 3 columns like below and then go to Ensemble -> Biomart section -> in Filtration section you could import this list and get fasta file based on selected regions. Chr Start End 12 100000 20000 ...
written 13 months ago by Whoknows650
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Software suggestion for RRBS DMR (methylation) analysis?
... Hi all, I have got a project on WGBS-RRBS data which preprocessed and I have no idea about softwares they have used, I just post some line here and let me know your opinion what software or R package I could use for DMR analysis/ downstream of these data: Please let me know: 1- What are these co ...
next-gen methylation rrbs written 13 months ago by Whoknows650
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Answer: A: Download genes from KEGG pathway
... Hi Some part of KEGG is not free anymore but your could try this [link][1] for downloading free section of the database. You could also search your genes in UniProt and find their relevant pathways in mapping section. [1]: http://www.kegg.jp/kegg/download/ ...
written 14 months ago by Whoknows650
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How to filter mutect2 VCF output?
... Hi I have ran mutect2 on a Blood and FFPE samples for finding somatic variations; Mutect2 found ~20k mutations, Actually, I'm new in cancer area and I wonder if anybody help me to find a way to reduce number of mutations. 1- Which field you suggest for filtration? 2- Can I use tool like Vcffilt ...
gatk alignment snp mutect2 written 15 months ago by Whoknows650 • updated 14 months ago by poisonAlien2.6k
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Comment: C: Urgent request - Pipeline for finding somatic and germline mutations of a cancer
... dear TriS thanks for your post, is was very constructive to me. ...
written 15 months ago by Whoknows650
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Urgent request - Pipeline for finding somatic and germline mutations of a cancer patient
... Hi all, This project belong to a patient and I need some fast helps for the analysis I have 2 WES samples from him, one of is Blood WES and another is cancer tissue WES. I just wanted to find germline mutation from Blood exome and also somatic mutation by comparing Blood and Cancer tissue samples, ...
exome next-gen snp written 15 months ago by Whoknows650 • updated 15 months ago by TriS3.4k
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Answer: A: How to obtain more GO terms for transcripts
... Dear Tom, The approach you have started is quite well for de-novo RNA-SEQ. As I have seen from these kinds of studies, GO term are generated much more than our real needs for a real biological facts. I think it doesn't matter how many GO terms you find the importance is how many were significantly ...
written 15 months ago by Whoknows650
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Comment: C: GO enrichment analysis with human ENSEMBL ids
... try David functional annotation, it works for human ...
written 16 months ago by Whoknows650
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Answer: A: GO enrichment analysis with human ENSEMBL ids
... Hi You could use [David Functional Annotation][1] or [enrichr][2], although enrichr works by Gene symbol, but you could easily convert Ensemble ID to gene symbol by [ensemble biomart][3]. [1]: https://david.ncifcrf.gov/ [2]: http://amp.pharm.mssm.edu/Enrichr/ [3]: http://www.ensembl.org/bi ...
written 16 months ago by Whoknows650
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Answer: A: NCBI vs Ensembl - which one to chose - for downloading protein fasta files
... None !! It is better to download from [UniProt][1], also you could download Refseq protein website NCBI, but in my experience UniProt gives more information and is much updated than NCBI and Ensemble. The other advantage of UniProt is you could obtain SWISS-prot manually curated entries or TrEMBL ...
written 16 months ago by Whoknows650

Latest awards to Whoknows

Popular Question 14 months ago, created a question with more than 1,000 views. For How to calculate average coverage for all genes
Popular Question 15 months ago, created a question with more than 1,000 views. For Finding isoform expression in RNA-Seq
Popular Question 16 months ago, created a question with more than 1,000 views. For Finding isoform expression in RNA-Seq
Scholar 16 months ago, created an answer that has been accepted. For A: Improve Large Heatmap Generation in R
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Finding orthologous gene within species
Appreciated 21 months ago, created a post with more than 5 votes. For A: What are the best gene prioritization tools?
Appreciated 21 months ago, created a post with more than 5 votes. For which one is better EdgeR or DEGSeq?
Great Question 21 months ago, created a question with more than 5,000 views. For Convert HTSeq count table to RPKM value using GFF/GTF
Good Question 21 months ago, asked a question that was upvoted at least 5 times. For Understanding up and down regulated genes from LOG2 foldchange or foldchange
Popular Question 21 months ago, created a question with more than 1,000 views. For Finding isoform expression in RNA-Seq
Popular Question 23 months ago, created a question with more than 1,000 views. For Finding isoform expression in RNA-Seq
Appreciated 24 months ago, created a post with more than 5 votes. For A: What are the best gene prioritization tools?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For which one is better EdgeR or DEGSeq?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For which one is better EdgeR or DEGSeq?
Centurion 2.1 years ago, created 100 posts.
Student 2.1 years ago, asked a question with at least 3 up-votes. For which one is better EdgeR or DEGSeq?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Finding orthologous gene within species
Popular Question 2.3 years ago, created a question with more than 1,000 views. For which one is better EdgeR or DEGSeq?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For which one is better EdgeR or DEGSeq?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to create color range for RPKM/FPKM using R?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For which one is better EdgeR or DEGSeq?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For which one is better EdgeR or DEGSeq?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Calculating RPKM for DESeq
Popular Question 2.9 years ago, created a question with more than 1,000 views. For which one is better EdgeR or DEGSeq?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Convert HTSeq count table to RPKM value using GFF/GTF

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