Tag: qualimap

Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation?

Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation? 0 I am working on RNASeq data for DE from a non-traditional organism (Artemia franciscana, a eukaryotic arthropod) whose draft genome was published last year. I should note here that although the genome was assembled with…

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is BBMap/Qualimap affected by log4j vulnerability

is BBMap/Qualimap affected by log4j vulnerability 2 no, unless the tools are used as a library in a web server. It’s worth noting picard.jar and abra.jar are affected (even though as Pierre L says, these are unlikely to be attacked on most systems). If you’re responsible for systems, esp web…

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QualiMap Multi-Sample BamQC does not load in center panel – usegalaxy.eu support

Dear @Mario_Garcia,The tool should work, I tested it right now with some test data. Please make sure: (a) your data was correctly analyzed by QualiMap BAM QC (i.e., the files should not be empty),(b) your files come from the same organism and data library(c) and you data has no weird…

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qualimap2 mean mapping quality

qualimap2 mean mapping quality 0 I’ve done a contrast experiment to see the difference between the bam with BQSR and the bam without BQSR. I use qualimap to evaluate both bams. This is the confusing part. Using hap.py and the giab na12878 truth vcf, shows the bam with BQSR is…

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Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

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