Bismark deduplication
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Bismark deduplication
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WebAug 11, 2024 · Aligned WGBS reads were deduplicated using the bismark_deduplicate command, and CpG methylation reports were generated using the bismark_methylation_extractor command with default parameters. cDMR and cLMR identification. Genome regional methylation rates were calculated using the methylKit R … WebContribute to Yonghao-Holden/tricks development by creating an account on GitHub.
WebJan 13, 2024 · What the UMI deduplication in deduplicate_bismark is doing is taking the chromosome, mapping orientation, start, end as well as the UMI sequence and check whether this exact combination was present already (in which case no further duplicates … Webdeduplicate_bismark. In its default mode it will use the first alignment for a given genomic region, which is basically equivalent to using a random alignment per position. The script works out whether the file to be deduplicated is a single-end or paired-end file. $ …
WebThe final step generates a report for each sample with the metrics on mapping, duplication rate and bias information. These reports can be downloaded to your laptop for viewing Here. However, it is more convenient to have the information for all samples in one report. WebMar 9, 2024 · We determined that while duplication of total reads was up to 95–97% in target regions according to Bismark deduplication reports (versus 15–17% duplicated reads across the genome for the three WGEM-Seq starling libraries, which suggests that sequencing optimization for this protocol might first focus post-capture before reducing …
Webdeduplication, methylation extraction, coverage file generation, and finally generates an aggregate MultiQC report. The workflow is suitable for 'standard' bisulfite sequencing experiments. Here is a graphical representation of the workflow: --- FastQC --- Trim Galore --- FastQ Screen --- FastQC --- Bismark --- Bismark deduplication
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