Tutorials

Tutorial: Analyzing differential expression of de novo assembled transcriptomes using RSEM

We already discussed assembly of single transcriptome in our Tutorial for RNA-Seq de novo assembly using Trinity. To compare transcriptomes of several samples, it is recommended to start analysis in slightly different way. At first you need to assemble transcriptome

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Tutorial: Analyzing differential expression of de novo assembled transcriptomes using RSEM

We already discussed assembly of single transcriptome in our Tutorial for RNA-Seq de novo assembly using Trinity. To compare transcriptomes of several samples, it is recommended to start analysis in slightly different way. At first you need to assemble transcriptome

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Tutorial: Ultrafast and accurate classification of metagenomic reads with CLARK (web interface)

Often, the construction of ultra-fast and precise taxonomic classifiers can compromise on their sensitivity (i.e., the number of reads correctly classified). CLARK is classification system able to taxonomically annotate short reads with high accuracy and high speed at the same

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Tutorial: Ultrafast and accurate classification of metagenomic reads with CLARK (web interface)

Often, the construction of ultra-fast and precise taxonomic classifiers can compromise on their sensitivity (i.e., the number of reads correctly classified). CLARK is classification system able to taxonomically annotate short reads with high accuracy and high speed at the same

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Tutorial: MapDamage Tool for Analysis of Ancient DNA Samples

If not hold in proper conditions (i.e. -20 °C or colder) – DNA rapidly degrades, its fragments become shorter and some bases disappear due to random hydrolyzes. Moreover, some bases turn into others bases due to deamination process. Methylated cytosine

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Tutorial: MapDamage Tool for Analysis of Ancient DNA Samples

If not hold in proper conditions (i.e. -20 °C or colder) – DNA rapidly degrades, its fragments become shorter and some bases disappear due to random hydrolyzes. Moreover, some bases turn into others bases due to deamination process. Methylated cytosine

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Tutorial: 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

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Tutorial: 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

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Learn How to Use GeneCoverage Tool to Evaluate Most Sequenced Species And Genes Within a Taxon Range (NCBI)

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

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Learn How to Use GeneCoverage Tool to Evaluate Most Sequenced Species And Genes Within a Taxon Range (NCBI)

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

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Learn how to use GATK and Picard to filter low quality variants in VCF files on human cancer data

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

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Learn how to use GATK and Picard to filter low quality variants in VCF files on human cancer data

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

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Benchmarking seven most popular genome assemblers

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 be covered in

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Benchmarking seven most popular genome assemblers

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 be covered in

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5 Unix commands every bioinformatician should know

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 rearrange the data in your files – change the delimiters,

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5 Unix commands every bioinformatician should know

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 rearrange the data in your files – change the delimiters,

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5 simple steps to make your research reproducible

If you want anyone to access and repeat your analysis consistently, regardless of the operating system, tool version or access to a computing cluster, you can use our sharing service. iMethods – Interactive Methods – will make your research reproducible.

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5 simple steps to make your research reproducible

If you want anyone to access and repeat your analysis consistently, regardless of the operating system, tool version or access to a computing cluster, you can use our sharing service. iMethods – Interactive Methods – will make your research reproducible.

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Samtools guide: learning how to filter and manipulate with SAM/BAM files

Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. In one

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Samtools guide: learning how to filter and manipulate with SAM/BAM files

Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. In one

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