User: shilparaopradeep

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Posts by shilparaopradeep

<prev • 18 results • page 1 of 2 • next >
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Tutorial: (Closed) InsideDNA: How to use BEDTools for analysis of genome methylation
... BEDTools is an extensive suite of utilities for genomic features analysis. There are several common genomic file formats, such as: BAM, GFF, GTF, VCF and most frequently BED which are used as an input for the BEDTools utilities. These utilities allow one to perform basic computing and comparison of ...
bioinformatics tutorial genomics written 2.8 years ago by shilparaopradeep180 • updated 2.8 years ago by Devon Ryan90k
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Tutorial: (Closed) InsideDNA: RNA-Seq de novo assembly using Trinity
... RNA-seq de novo assembly is one the most frequent type of sequence analysis in biology and bioinformatics. However, just as a complete genome assembly, RNA-seq assembly is not trivial and often requires large amount of RAM and CPUs. In this tutorial, we explain how to use one the most popular RNA-se ...
genome bioinformatics tutorial written 2.9 years ago by shilparaopradeep180
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Tutorial: (Closed) InsideDNA: Benchmarking seven most popular genome assemblers
... Introduction: metrics for genome assembly comparison Several factors influence performance of de novo genome assemblers: read coverage, GC-content, repeats fraction, etc. This report aims to elucidate the effect of read coverage on the performance of de novo assemblers, while the other aspects will ...
bioinformatics tutorial insidedna genomics written 2.9 years ago by shilparaopradeep180 • updated 2.9 years ago by Devon Ryan90k
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Tutorial: (Closed) InsideDNA: Evaluating which species and genes are most sequenced within a taxon range in NCBI database with geneCoverage
... One of the common burdens for evolutionary biologists dealing with phylogeny reconstruction is supplementing newly sequenced data with sequences already available in GenBank. This exercise is particularly common when one would like to build a large(r) phylogenetic tree. Here we present a small pipel ...
bioinformatics tutorial genomics written 2.9 years ago by shilparaopradeep180 • updated 2.9 years ago by Devon Ryan90k
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Tutorial: (Closed) InsideDNA: 5 Unix commands every bioinformatician should know
... Bioinformaticians often have to manage large text files containing reads, sequences of genomes, alignments, genetic variants, and so on. Sometimes the files you receive do not have quite (or indeed at all) the same format required by tools used in the downstream analysis. In such cases you have to r ...
bioinformatics tutorial genomics written 2.9 years ago by shilparaopradeep180 • updated 2.9 years ago by Devon Ryan90k
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Tutorial: (Closed) InsideDNA: How to use GATK and Picard to filter low quality variants?
... Information on genetic variants in a sample – meaning the differences between a sample and a reference genome – are generally stored in a form of VCF files. Unfortunately, the structure of VCF files is not standardized; VCF files can include various characteristics of genetic variants; files can be ...
bioinformatics tutorial genomics written 2.9 years ago by shilparaopradeep180 • updated 2.9 years ago by Devon Ryan90k
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Tutorial: (Closed) InsideDNA: Improving quality of raw fastq data with Trimmomatic and RemoveBadTiles
... Reads cleaning and filtering is an important pre-processing step of the raw sequencing data. In our previous tutorial we explored the quality of the raw sequencing data and demonstrated how to correctly interpret results from the FastQC quality reports. Based on the results of the quality assessment ...
bioinformatics tutorial genomics written 3.0 years ago by shilparaopradeep180 • updated 2.9 years ago by Devon Ryan90k
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Tutorial: (Closed) InsideDNA: Analysing raw sequencing reads with FASTQC for quality control and filtering
... Quality control and filtering of sequencing reads is one of the most important steps in the pre-processing of sequencing reads. However, it is not always trivial to figure out which reads needs adjustment and which can be left untouched. In this tutorial, we explain the basics of the Phred score con ...
tutorial bioinfromatics genomics written 3.0 years ago by shilparaopradeep180 • updated 2.9 years ago by Devon Ryan90k
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Tutorial: (Closed) InsideDNA: Analysing transcription factors with ChIP-Sequencing data: a full bioinformatics pipeline and an example of Candida fungal pathogen
... The phenotype of an organism depends not only on its genomic sequences, but also on the activity of its genes or, in other words, on gene expression levels. Gene expression, in turn, is determined by the structure of chromatin – a complex aggregate of DNA and proteins that forms chromosomes. Various ...
bioinformatics tutorial written 3.1 years ago by shilparaopradeep180 • updated 2.9 years ago by Devon Ryan90k
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Tutorial: (Closed) InsideDNA: Running approximate Bayesian computation inferences about population history for RAD-seq data
... One of the most powerful frameworks for inference of population genetics or genomics scenarios is Approximate Bayesian Computation (ABC). Compared to conventional approaches such as likelihood-based ones, ABC-based strategy allows to effectively model complex population history scenarios and offers ...
bioinformatics tutorial written 3.1 years ago by shilparaopradeep180 • updated 2.9 years ago by Devon Ryan90k

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