User: inambioinfo

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inambioinfo30
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Posts by inambioinfo

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How Splice Junction database(SJ.out.tab) is generated from GTF(ENSEMBL) and Reference Genome (GRCh38) using STAR Aligner during Genome indexing
... As am not an expert in the field, Hence I could like to know few basic concept on how STAR generate Splice Junctions Database(sjdb/SJ.out.tab) while indexing the reference genome with gtf file. I find information from STAR Manual: http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR ...
gtf hisat star splice junction assembly written 3 months ago by inambioinfo30 • updated 4 weeks ago by Biostar ♦♦ 20
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... You are right, I shall go through all the content and will get back to you. Thanks ...
written 3 months ago by inambioinfo30
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... Seems there are no similarities between the network propagation based algorithm to the MCL clustering algorithm. I will be trying to get the cancer driver genes list from HIT'nDRIVE using genomics data. Later, I have 2 options : 1. I shall convert those genes to frame translation and search with t ...
written 3 months ago by inambioinfo30
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Comment: C: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... I have my own Genomics and Proteomics Data from the same patient sample. I should give a try with that and let you know. ...
written 3 months ago by inambioinfo30
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Comment: A: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hit
... Thanks for sharing and am really interested in working on this. I have a query: Can we able to get proteomics level information for those driver genes. ...
written 3 months ago by inambioinfo30
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Answer: A: Mapping GRCh38 to ENSEMBL / UCSC ,Gene, transcript , cDNA and Protein IDs and Se
... Hi Ben, Thanks for your information. Am curious about few things and could like to make things clear. Do i need to use the GTF file for mapping from ENSEMBL Database: http://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz or http://ftp.ensembl.org/pub/release-87 ...
written 10 months ago by inambioinfo30
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Mapping GRCh38 to ENSEMBL / UCSC ,Gene, transcript , cDNA and Protein IDs and Sequence
... Hello Folks, I am interested in mapping latest Genome GRCh38 to other standard databases such as ENSEMBL, UCSC and RefSeq. As of now, i have GRCh38 in hand. I could like to know which all the files i need to have with me from the above database to map back to the complete genome with corresponding ...
genome mappping rna-seq snp ensembl written 10 months ago by inambioinfo30 • updated 10 months ago by Ben_Ensembl510
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Answer: A: hg38 annotation file (gtf) UCSC format
... My answer may be very late, But still it will be usefull for someone who are in need. UCSC Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables If Human then Clade : Mammal Genome : Human Assembly : latest one (Currently GRCh38/hg38) Group : Genes and Gene Predictions Track : RefSeq Gene ...
written 10 months ago by inambioinfo30
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Rna Seq To Protein Seq Conversion
... Hi,Am new here to the group and probably my first question as a Newbie to RNA seq data analysis. I have three question to ask here. May i get any workflow to process my FASTQ file and get expression analysis (this is basic question I know but am not aware which tool i have to use and there are man ...
proteomics rnaseq rna written 3.8 years ago by inambioinfo30 • updated 3.8 years ago by Devon Ryan73k

Latest awards to inambioinfo

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: hg38 annotation file (gtf) UCSC format
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Rna Seq To Protein Seq Conversion

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