User: Amitm

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Amitm2.0k
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Posts by Amitm

<prev • 252 results • page 1 of 26 • next >
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Comment: C: How to identify mRNA 3' UTR by bulk RNA-seq data
... Hi, If your organism of interest has reference annotation available (like genome sequence and gene information in [GTF format][1]), then a transcriptome assembly followed by mapping, should give you genomic coordinates of 5' and 3' ends _as per your data.. when seen through prior knowledge of availa ...
written 12 days ago by Amitm2.0k
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Comment: C: Platypus variant caller error
... Hi, Unless there is a specific reason to build the package yourself, you could take the [conda][1] route and install many bioinfo. related packages through one command-line step. The related page for platypus is [here][2]. Advantage of using conda is that it takes care of all software dependencies. ...
written 24 days ago by Amitm2.0k
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Comment: C: how to interpret a CNV scatter plot
... No worries. To understand better the outcome in pat.C, I would recommend to look into the 'segmentation' output from which these plots are made. It should be in a format similar to chrStartEndseg.meanmarker support That should tell what those two small segments in pat.C are like. The genomic ...
written 4 weeks ago by Amitm2.0k
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Answer: C: how to interpret a CNV scatter plot
... Hi, I am assuming that this is from sequencing-based approach. PatientB has a very strong signal for a deletion segment spanning ~30thMb to 60th Mb region, which includes your gene. PatientC appears to have a deletion signal but which appears to be focal around CCR4 only. The orange line is the 'se ...
written 4 weeks ago by Amitm2.0k
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Comment: C: Annotating VCF files
... Hi, With that many VCF files to annotate, it would be best to have a local installation of a variant annotation program. I haven't used wANNOVAR, but VEP and SNPEff are extensively documented. If you were to install [VEP][1]/ [SNPEff][2], it would be easiest to go through the [(bio)conda package res ...
written 5 weeks ago by Amitm2.0k
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Comment: C: Creating bed file for gene specific variant extraction from VCF file
... Hi Karthick, Of course GRCh38 is now the default on genome browsers, but you could access the '37' by clicking the `View in archive site` link at the very bottom right-hand side of Ensmbl page. Alternatively, [this][1] is the direct link. The BioMart that you would access there would have GRCh37 dat ...
written 5 weeks ago by Amitm2.0k
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Comment: C: De novo transcriptome from PE reads with high multi-mapping rate (Bowtie2)
... Hi, Any specific reason for asking to return (upto) 20 algn. per pair, using `-k 20` ? I would think that using either of these combinations would be better - 1) `-k 1 --best` (hard thresholding to return only 1 algn. and the best one at that. 2) Or, if not wanting to hard threshold to return only 1 ...
written 5 weeks ago by Amitm2.0k
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Answer: A: Creating bed file for gene specific variant extraction from VCF file
... Hi, That is because the annotation data is transcript-centric and hence multiple (transcript ID) accessions per gene. I do not know of any way to collapse the output to gene-level. But, you could do that using [Ensembl BioMart][1]. Under the "Attributes" section (left-hand menu), for the "Features" ...
written 6 weeks ago by Amitm2.0k
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Comment: C: WES or WGS
... Hi, Some of the things which I understand. If you are going to talk about mutations that are affecting protein-coding sequences then there is no advantage of WGS over WES. In any case, these are some of the things that could be done by WGS (and not standard WES) - 1) Fusion genes - Many a times the ...
written 6 weeks ago by Amitm2.0k
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Comment: C: how to get the installation histort of conda
... Hi, You could use this cmd - conda list --revisions That would list out pkgs installed by date. Though, there would be other communities better suited for this question. ...
written 7 weeks ago by Amitm2.0k

Latest awards to Amitm

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 7 weeks ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How to decide the quality of RNA-seq analysis
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Popular Question 7 months ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Scholar 8 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 9 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 9 months ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Scholar 2.2 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 2.7 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 2.8 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Kmer Content in FastQC failed
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Removing PCR primers in targeted sequencing with nested amplicons
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Scholar 3.5 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Somatic allele frequency from TCGA
Good Answer 3.6 years ago, created an answer that was upvoted at least 5 times. For A: Kmer Content in FastQC failed
Scholar 4.1 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling
Scholar 4.1 years ago, created an answer that has been accepted. For A: Non-cancer somatic mutation calling

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