User: hkarakurt

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hkarakurt110
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Posts by hkarakurt

<prev • 66 results • page 1 of 7 • next >
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Genomic Variant calling from RNA-Seq Data
... Hello everyone, I started to work on variant calling from RNA-Seq data. As I understood from the papers and messages I read, using RNA-Seq is a challange due to high noise in RNA-Seq data. I tried GATK4 pipeline (even it is said that the pipeline is for germline mutations) they posted in website as ...
genomic variant rna-seq snp written 3 days ago by hkarakurt110
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Comment: C: Optimal Number of SNPs in NA12878 WES Data
... Hello, NIST gold standard VCF is coming from WES and WGS experiments as I know. Actually, our advisor said 1.3 million (1.6 with False Positives) SNVs are too many for a single WES experiment. For all 20 WGS data for the same individual, NA12878, total SNV (with False Positives) are 3 million. Tha ...
written 10 weeks ago by hkarakurt110
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Optimal Number of SNPs in NA12878 WES Data
... Hello everyone, I downloaded one of the NA12878 WES data, SRR098401, from NCBI FTP server with sratoolkit. I used BWA-MEM to align it to hg19 and GATK best practices to obtain VCF that only contain SNVs. I did not use any filtering. After I obtain VCF, I compared it with NISTv3.3.2 (ftp://ftp-trace ...
gatk wes snp written 10 weeks ago by hkarakurt110
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Calculating GC content around a specific genomic location
... Hello everyone, I am looking for a method that calculates GC content of a specific genomic region. I could not find an automated Python (or R) library that calculates GC content around a location. For example; I want the GC contect of + and - 20bp around Chr3 16500 location. Is it possible to do it ...
genome wgs gc wes snp written 11 weeks ago by hkarakurt110 • updated 11 weeks ago by benformatics2.0k
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
... Hello everyone, First, I am so sorry if my post title does not correspond to my post completely. I am using scater/scran package for scRNA-Seq analysis and MNN for batch correction. As I know with multiple datasets; MNN integrates first and second datasets first and integrate the third one with fi ...
scrna-seq batch correction rna-seq written 3 months ago by hkarakurt110
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Trimmomatic trims most of the reverse strand
... Hello everyone, I have a paired-end data. It is from small part of human genome not a WGS or WES. I use BWA for alignment and do variant calling. Since I had some false positives I wanted to do trimming. I used trimmomatic with command: trimmomatic PE -phred33 -threads 2 read1.fastq.gz read2.f ...
trimmomatic fastq trim bwa written 4 months ago by hkarakurt110 • updated 4 months ago by GenoMax96k
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Comment: C: SNPs on a single transcript of a gene with multiple transcripts
... It was a hypothetical question. I meant if only one transcript of a gene have a SNP, how should I treat it? Is there any "main transcript annotation" of a gene or a scoring system. ...
written 6 months ago by hkarakurt110
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SNPs on a single transcript of a gene with multiple transcripts
... Hello, I am doing WGS analysis and I have a question. As you know some genes have multiple transcripts in the genome. E.g. BRCA1 has about 30 transcripts. As I understand one of the transcripts is enough to produce the related protein and transcription of the transcript is highly associated with tis ...
gene wgs wes snp written 6 months ago by hkarakurt110 • updated 6 months ago by caggtaagtat1.4k
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Comment: C: Network Analysis of Each Cluster of Protein Interaction Network
... Thank you for your answer. I am already using igraph but as I know it does not have a function to extract and analyze the subset of main graph. I can try with a for loop. ...
written 7 months ago by hkarakurt110
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Comment: C: Network Analysis of Each Cluster of Protein Interaction Network
... Thank you for your answer. I can use Cytoscape to analyze a subset of nodes but as I mentioned for more than 50 cluster (can go up to 350) it would be really time consuming activity. I am more like looking for a way to analyze each cluster with single function. ...
written 7 months ago by hkarakurt110

Latest awards to hkarakurt

Great Question 9 weeks ago, created a question with more than 5,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 4 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Epic Question 5 months ago, created a question with more than 10,000 views. For Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
Popular Question 6 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 7 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Great Question 16 months ago, created a question with more than 5,000 views. For Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
Great Question 16 months ago, created a question with more than 5,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
Popular Question 16 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 16 months ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 16 months ago, created a question with more than 1,000 views. For How to extrach gene names and peaks from BedGraph or BigWig files
Popular Question 16 months ago, created a question with more than 1,000 views. For Cufflinks gives only CUFF names with a gtf.
Popular Question 16 months ago, created a question with more than 1,000 views. For Differential ChIP-Seq Analysis
Student 16 months ago, asked a question with at least 3 up-votes. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
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Popular Question 19 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 19 months ago, created a question with more than 1,000 views. For How to extract expression data from RAW data.
Popular Question 19 months ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 19 months ago, created a question with more than 1,000 views. For Differential Coexpression Analysis
Student 20 months ago, asked a question with at least 3 up-votes. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 22 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 23 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis

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