User: hkarakurt
hkarakurt • 110
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Posts by hkarakurt
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... 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 ...
written 3 days ago by
hkarakurt • 110
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... 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
hkarakurt • 110
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... 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 ...
written 10 weeks ago by
hkarakurt • 110
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... 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 ...
written 11 weeks ago by
hkarakurt • 110
• updated
11 weeks ago by
benformatics • 2.0k
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... 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 ...
written 3 months ago by
hkarakurt • 110
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... 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 ...
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... 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
hkarakurt • 110
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... 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 ...
written 6 months ago by
hkarakurt • 110
• updated
6 months ago by
caggtaagtat • 1.4k
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... 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
hkarakurt • 110
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... 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
hkarakurt • 110
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