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GDC: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
- features we'd like to support: snv, indel, structural variants, extra chromosomal dna
- create ta…
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If I have files output from AA and AC, is there a way for me to experiment with the cycle view /genome browser to investigate potential larger structures formed from my cycles/paths? Would be good if …
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v0.4.13
The coordinate in cycle file is, for example,
chr1 100 *500*
however, in the eccDNA_x_intervals.bed output file, it becomes
chr1 100 **501**
for other outputs, like BFB_x_intervals.…
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Hi,
Thanks very much for sharing this tool to parse AmpliconArchitect (AA) results. My original understanding about AA's *cycles.txt file is that if a cycle include segment 0 at the start and at th…
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Hi,
I run this useful tool and an error occurs as follows:
Traceback (most recent call last):
File "/ATAC-amp/AtacAmp.py", line 303, in
split_bk_dir = process_split_reads(split_bam_f)
Fi…
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Hello,I meet a question when I run AA for getting data.
The AmpliconArchitect version is 1.2
my command:
python /home/tang/tools/AmpliconArchitect/src/AmpliconArchitect.py --bed ../NCI-H716_…
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Hi Jens,
I am using AmpliconSuite for a set of cancer WGS data. I have 36 samples, most of them finished successfully. But there are 10 of them that have been running for 5 days. And still not finis…
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Hello,
I have generated WGBS/ATAC data for my samples but no WGS data. Is WGBS/ATAC data valid input for AA?
Both data are often used to infer CNV so I guess WGBS/ATAC might produce a concordant …
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H Xiaotao, great tool filling an urgent unmet need.
I am running neoloopfinder on the following SVs:
```
chr1 chr1 ++ 198179654 205207358 translocation
chr1 chr1 …
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1. Sometimes after running AA and getting ecDNAs, we also want to find some somatic mutations or allele-based CNA and so on, so the RG tag in bam is mostly important ! In order to reuse the bam file f…