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Hi Viraj,
Thanks for your work in AA. Do you know what happened about this error? Thanks for your help.
$]cat test_out.bed
7 54700000 54950000 30.0 /dfs3/weil21-lab/yac7/data/test.bed
#####…
YaCui updated
4 years ago
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I have some samples -only tumour, no any normal samples as control, and here is my code for these pipeline, it's OK?
python3 /share/home/luoylLab/zengyuchen/biosoft/AmpliconSuite-pipeline/PrepareAA…
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Hi,
I hope this message finds you well. I'm reaching out to seek your assistance regarding an error I encountered while using Circlehunter to identify extrachromosomal DNA (ecDNA) in my ATAC-seq da…
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Dear,
I am using Circle-map to predict ecDNA,My data is download from SRA (for example, https://www.ncbi.nlm.nih.gov/sra/?term=SRR9089606). I firstly downsample this data to about 10X by seqtk like …
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Hi,
I have a question about potential filtering steps for the decoil output.
I used Decoil on a sample and found 43 ecDNA, which was more than I was expecting. I have also used coral on the same…
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Hi, recently I was trying to use Circle-Map to analyze WGS data on GEO. And I got 20 "my_unknown_circle.bed" files following "Identification of circular DNA using Circle Map Realign" tutorial. The who…
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Hello,I meet a question about prepare the bed file for AA.
my command:
python /home/tang/tools/PrepareAA/PrepareAA.py -s A549 -t 4 --cnvkit_dir /home/tang/tools/cnvkit/cnvkit.py --sorted_bam /home…
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Hi.
I have applied the program in WGS data of several cell lines. I started from .fastq files and used PrepareAA.py to generate CNV calls. However, all of these runs generated empty AA_CNV_SEEDS.bed…
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Hi,
when I call CNVs using CNVkit, need to consider sample purity and ploidy to caculate absolute copy number?
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Thanks for developing this tool for ceDNA analysis. I have some bam files from generated from WGBS data and am wondering if AmpliconSuite is able to use these bam files as input for ceDNA detecion? If…