User: seta

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seta1000
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Posts by seta

<prev • 609 results • page 1 of 61 • next >
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Comment: C: Why there are some discrepancies between VEP output and "variation" section of E
... Thank you very much for your helpful info. ...
written 3 days ago by seta1000
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Comment: C: hormone information and secondary metabolite biosynthesis pathway information fo
... Please take a look at [enter link description here][1]. [1]: https://www.genome.jp/kegg/kaas/ ...
written 8 days ago by seta1000
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Comment: C: Why there are some discrepancies between VEP output and "variation" section of E
... Thank you for all the comments. Could you please kindly tell me how I can obtain the minor allele in various populations, say Asian, European, etc? Regarding the allele and strand, STRAND defined as the DNA strand (1 or -1) on which the transcript/feature lies at [enter link description here][1]. I ...
written 8 days ago by seta1000
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Answer: A: hormone information and secondary metabolite biosynthesis pathway information fo
... You can use KAAS server for mapping genes with KEGG pathway and find which genes involved in the pathways of interest. ...
written 8 days ago by seta1000
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Why there are some discrepancies between VEP output and "variation" section of Ensembl?!
... Hi all, I used VEP from Ensembl to annotate a list of SNP derived from whole genome sequencing of a population. When I examined some of them, I found there are some differences between VEP output and what "variation" section of ensembl showed us. For example, the strand for rs104895094 determined m ...
alternative allele ensemble vep output snp written 8 days ago by seta1000 • updated 5 days ago by Emily_Ensembl15k
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Comment: C: Microbial diversity analysis using whole-genome metagenomic data
... Hi all, Long delay, but may be helpful. I was wondering how I can study the microbiome (say microbial flora) from whole genome sequencing data of healthy people belong to a given population? Please kindly let me know your suggested procedure, any pipelines? Thank you ...
written 23 days ago by seta1000
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Comment: C: Please suggest an appropriate genome-guided transcriptome assembler
... Thank you, Kevin. For alignment, I used STAR, it sounds great. However, my issue is the genome-guided assembler, as I said in my previous comment, the results of STAR/cufflinks and STAR/Stringtie are so different, Stringtie created few genes compared to cufflinks, I don't know why it missed lots of ...
written 4 weeks ago by seta1000
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Comment: C: Please suggest an appropriate genome-guided transcriptome assembler
... Yes, here, biostar forum, I don't exactly remember why. However, I performed genome-guided transcriptome assembly with two programs, cufflinks and stringtie and obtained so different results. It sounds stringtie miss a lot of genes, unlike cufflinks. ...
written 4 weeks ago by seta1000
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Please suggest an appropriate genome-guided transcriptome assembler
... Dear all, I have RNA-seq data generated by Illumina Hiseq 2000 as 100bp, PE from human, control and diseased samples. I'm looking for polymorphic simple sequence marker (SSR) between two groups of control and disease. I'm going to do genome-guided transcriptome assembly for each group, then survey ...
genome marker alignment rna-seq written 4 weeks ago by seta1000 • updated 4 weeks ago by Kevin Blighe24k
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Comment: C: Please provide me your comments on the variant calling in this case
... Hi Kevin, Thank you very much for your explanation. Yes, I have fastq files. I'm aware of phased vcf file that alleles separated with pipe sign (|). As I searched, there are various tools that get phased vcf file as input and extract the haplotype as fasta format. Assuming gene X and its varian ...
written 6 weeks ago by seta1000

Latest awards to seta

Guru 8 days ago, received more than 100 upvotes.
Great Question 9 days ago, created a question with more than 5,000 views. For Remove unwanted characters from FASTA file
Student 16 days ago, asked a question with at least 3 up-votes. For rRNA contamination in poly A-enriched libraries
Popular Question 22 days ago, created a question with more than 1,000 views. For Please help with comparing several gene ontology (GO) list
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