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Hello developers!
I'm running Clair3 on WGS data from tumor biopsies. I'm a but confused to how variants are reported in the merge_output.vcf file. In the example below, two variants can be seen wi…
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Hello,
I am utilizing a scTCR protocol where it uses dual indexing to barcode each cells. Basically, the protocol states,
"the amplification reaction contains flanking rhPCR primers ([Suppleme…
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Hi, @ShixiangWang
We want to analyze the purity and ploidy of a set of tumor samples using panel sequencing data (over 700 genes). The segment files were from CNVkit and maf files were from Mutect2 …
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I appreciate you changing the name of the argument and keeping both ways of saying it as valid options. I noticed the name of the process still says tags though. Would you consider changing it to indi…
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Hi Eric,
I'm not quite sure about the average read length of our RNA-Sequencing data. The company we sent for RNA sequencing has written the below text " After cluster generation, the library prepa…
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### Data Owner Name
National Human Genome Research Instititue
### Data Owner Country/Region
United States
### Data Owner Industry
Life Science / Healthcare
### Website
https://hu…
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Hi everyone,
I have an issue with the CRISPResso analysis of some of my NGS samples (Input: paired end fastq files, amplicon sequence and gRNA added).
The goal is to see the editing efficiency…
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To accommodate non-Illumina sequencing data, create an option to skip Trimmomatic or substitute with fastp
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I just started using TrimeGalore for our RRBS sequencing and I wrote a short slurm script to run to but I keep getting this error message: _Please provide an even number of input files for paired-end …
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Hello,
thanks for making PGGB, I have a question, I am running an analysis and would like to align 18 species of catfish, they are diploid individuals however when curling the assemblies GCA in ge…