User: toralmanvar

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toralmanvar650
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Posts by toralmanvar

<prev • 138 results • page 1 of 14 • next >
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Comment: C: Bedtools intersect alternatives available
... But what is the purpose? For some of the task "grep -f" or "join" command can also be used. ...
written 28 days ago by toralmanvar650
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Comment: C: Could I call peaks without input control for histone modification's data?
... Yes you can use any software of your choice for comparative ChIPSeq analysis but, using input control have its own advantage like removing the bias occurring during the enrichment and sequencing process. i.e it is always needed to distinguish background noise from enriched signals. ...
written 28 days ago by toralmanvar650
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Comment: C: Extracting snps from a range of coordinates
... How you have identified the genes? means have you used any specific tool for gene prediction? ...
written 29 days ago by toralmanvar650
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Comment: C: Problem to Understand the visualization of IGV
... Can you highlight the portion which you are looking for in the image? ...
written 4 weeks ago by toralmanvar650
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Answer: A: Extracting snps from a range of coordinates
... If you have the gtf/gff3 file of gene annotation along with variant's .vcf file then I will suggest you to annotate your variants using [snpeff][1] as it will not only provide information on which SNPs belongs to which gene but it will also determine the effect of the variants. [1]: http://snpe ...
written 4 weeks ago by toralmanvar650
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Answer: A: navigate IGV to the points of interest
... You can first convert your BAM file in to BED file using [bamtobed][1] and can get position of chromosomes where reads are mapped. [1]: https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html ...
written 5 weeks ago by toralmanvar650
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Answer: A: CNV calling from exome sequencing data with a low number of samples
... CNVKIT is a good pipeline to consider for CNV anaysis. You can also give try to [VarScan][1] [1]: http://varscan.sourceforge.net/ ...
written 5 weeks ago by toralmanvar650
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Comment: C: Phenotypic Variation Explained By Snps In Gwas
... Thank you for the reply. But, my main concern is obtaining the phenotypic variance (var %) using the gwaa.R (GenABLE) result which I have for each trait separately. It contains 5 columns as shown below: - SNP - Estimate - Std.Error - t-value - p-value i.e I got the list of significant S ...
written 5 weeks ago by toralmanvar650
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Comment: C: MiSeq or HiSeq for metatranscriptome sequencing
... When you consider transcriptome for study, then read length of 2x150 bp is enough ([reference][1]) to get good assembly unlike genome analysis where you can obtain good results with increased read length. As you are working with metagenome you can focus more on considering more read depth so as to i ...
written 5 weeks ago by toralmanvar650
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Comment: C: replacement for Arlequin
... Ok, then you can try Genepop. It work in windows, Macs as well as linux. ...
written 5 weeks ago by toralmanvar650

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to extract specific rows based on row number from a file
Scholar 5 weeks ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file
Scholar 3 months ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file
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