User: igor

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igor4.4k
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Posts by igor

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Answer: A: How to extract only TUMOR variants from vcf file?
... There are instructions given in the [VarScan documentation][1] for extracting somatic mutations: > The latest release of VarScan includes a new (undocumented) subcommand > that will separate a somatic output file by somatic_status (Germline, > Somatic, LOH). Somatic mutations will further ...
written 29 days ago by igor4.4k
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... I don't think they check the contents of your files other than to make sure they are in the proper format. ...
written 29 days ago by igor4.4k
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Comment: C: Bioinformatician salary - Current market
... See also: https://www.glassdoor.com ...
written 7 weeks ago by igor4.4k
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Comment: C: 10x Supernova de novo assembly
... More importantly, they came out with a new version of the reagents (v2). We had multiple failed assemblies with v1, but all worked with v2. ...
written 7 weeks ago by igor4.4k
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Comment: C: What is contained in the GRCh38 reference, and how was it constructed?
... Keep it mind that the original reference human genome was completed in 2003. Many people have been working on improving it ever since, so it's a lot of work. ...
written 8 weeks ago by igor4.4k
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Comment: C: How detrimental are duplicate reads in RNAseq experiments?
... Good find. However, the paper mostly discusses single-cell RNA-seq. Regarding normal bulk RNA-seq, they say: > In the Illumina labs, the team also experimented with purposefully > generating a large number of PCR duplicates. The team compared data > from unique reads and duplicates—'good' ...
written 8 weeks ago by igor4.4k
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Comment: C: FASTQ to SAM File converter
... Definitely faster than some of those fancy aligners. ...
written 9 weeks ago by igor4.4k
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Comment: C: overlap BED files, but account for region name
... Thanks for confirming. I just wanted to make sure I am not reinventing the wheel or missing something. ...
written 9 weeks ago by igor4.4k
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Comment: C: FASTQ to SAM File converter
... You should figure out exactly what you are trying to do and understand the whole process before trying to find "the fastest tools". ...
written 9 weeks ago by igor4.4k
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overlap BED files, but account for region name
... I recently found ReMap which is a great resource of TF binding sites across different studies. They [provide][1] the binding sites in BED format where each region is named based on the TF. Although it's relatively trivial to overlap two BED files (using something like `bedtools fisher` or `bedtools ...
overlap bed bedtools written 9 weeks ago by igor4.4k • updated 9 weeks ago by Chris Miller18k

Latest awards to igor

Teacher 28 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Student 7 weeks ago, asked a question with at least 3 up-votes. For ATAC-seq peak calling with MACS
Great Question 7 weeks ago, created a question with more than 5,000 views. For ATAC-seq peak calling with MACS
Scholar 11 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 3 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Appreciated 3 months ago, created a post with more than 5 votes. For A: read length of sequence
Appreciated 3 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Popular Question 3 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Popular Question 4 months ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 4 months ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 5 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data

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