ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data

Esse, Ruben; Grishok, Alla

doi:10.1101/220079

Cited by 2 publications

(2 citation statements)

References 20 publications

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“…However, they do not collect the data to a single-click loadable visualisation, including all the metrics and analysis reports (for tool comparisons, see Supplementary Table 1) and therefore are more time consuming and require higher levels of computational expertise of the user. Other solutions provide GUI-based analysis, where modifying the source code is more time consuming [9][10][11] . Promising database-based all-inclusive data analysis platforms have been developed 12,13 , but these are feasible for only large core facilities, where the time and effort necessary for system administration and database management becomes cost-effective.…”

Section: Introduction and Resultsmentioning

confidence: 99%

NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

Telenius

Hughes

2018

Preprint

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With decreasing cost of next-generation sequencing (NGS), we are observing a rapid rise in the volume of 'big data' in academic research, healthcare and drug discovery sectors. The present bottleneck for extracting value from these 'big data' sets is data processing and analysis. Considering this, there is still a lack of reliable, automated and easy to use tools that will allow experimentalists to assess the quality of the sequenced libraries and explore the data first hand, without the need of investing a lot of time of computational core analysts in the early stages of analysis.NGseqBasic is an easy-to-use single-command analysis tool for chromatin accessibility (ATAC, DNaseI) and ChIP sequencing data, providing support to also new techniques such as low cell number sequencing and Cut-and-Run. It takes in fastq, fastq.gz or bam files, conducts all quality control, trimming and mapping steps, along with quality control and data processing statistics, and combines all this to a single-click loadable UCSC data hub, with integral statistics html page providing detailed reports from the analysis tools and quality control metrics. The tool is easy to set up, and no installation is needed. A wide variety of parameters are provided to fine-tune the analysis, with optional setting to generate DNase footprint or high resolution ChIP-seq tracks. A tester script is provided to help in the setup, along with a test data set and downloadable example user cases.NGseqBasic has been used in the routine analysis of next generation sequencing (NGS) data in highimpact publications 1,2 . The code is actively developed, and accompanied with Git version control and Github code repository. Here we demonstrate NGseqBasic analysis and features using DNaseIseq data from GSM689849, and CTCF-ChIP-seq data from GSM2579421, as well as a Cut-and-Run CTCF data set GSM2433142, and provide the one-click loadable UCSC data hubs generated by the tool, allowing for the ready exploration of the run results and quality control files generated by the tool.Availability: Download, setup and help instructions are available on the NGseqBasic web site

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Section: Introduction and Resultsmentioning

confidence: 99%

NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

Telenius

Hughes

2018

Preprint

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“…GRO-seq data was obtained from the NCBI GEO database (GSE47132) and the reads were mapped to the C. elegans genome (ce10 assembly) using ChIPdig, a software application to analyze ChIP-seq data (Esse and Grishok 2017). Then, reads matching ribosomal RNA loci were removed, as described before (Cecere et al 2013).…”

Section: Analysis Of Gro-seq Datamentioning

confidence: 99%

DOT1L suppresses nuclear RNAi originating from enhancer elements in Caenorhabditis elegans

Esse

Gushchanskaia

et al. 2018

Preprint

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Summary 7Methylation of histone H3 lysine 79 (H3K79) by DOT1L is associated with actively 8 transcribed genes. We have previously demonstrated that DOT-1.1, the Caenorhabditis 9 elegans DOT1L homologue, cooperates with the chromatin-binding protein ZFP-1 10 (homologue of the mammalian AF10) to negatively modulate transcription of highly and 11 widely expressed target genes. Also, zfp-1 deficiency has been associated with reduced 12 RNA interference (RNAi) response. In addition, in MLL-rearranged leukemia, H3K79 13 methylation at homeobox genes was shown to antagonize repressive chromatin marks. 14 Here, we connect these various manifestations of DOT1L function. We demonstrate that 15 DOT1L suppresses transcription at enhancers, thereby preventing double-stranded 16 RNA (dsRNA) formation and ectopic histone H3 lysine 9 (H3K9) methylation. Moreover, 17we show that lethality of dot-1.1 mutant worms is suppressed by mutations in the RNAi 18 pathway, suggesting ectopic activation of endogenous RNAi in the absence of DOT1L.

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ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data

Cited by 2 publications

References 20 publications

NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

DOT1L suppresses nuclear RNAi originating from enhancer elements in Caenorhabditis elegans

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