AmpliconSuite-pipeline

AmpliconSuite-pipeline copied to clipboard

How to understand different results of AmpliconArchitect in different servers?

5

Hi, I Ran the AS-pipeline for the bam that my colleague has run by AA(1.2_r2) and AC (0.4.13) but got different results, then I considered it as a version problem....

JFanbio

how the pipeline generate CNV_CALLS_pre_filtered.bed file?

8

Hi there, I used the end-to-end wrapper to process my data, but I didn't get any ecDNA. So, I want to check the steps one by one. I reran the...

JFanbio

There are some small bugs in singularity running scripts

1

1. If the singularity version number is a strange number like "singularity-ce version 3.11.5-1.el7", then the original function `test_singularity_version` will get a singularity_version like "3.11.5-1.el7", but the `5-1` is impossible...

panxiaoguang

run Ampliconsuite-pipeline on WGBS data

8

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...

QLZhouBio

cycle view

1

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...

eesiribloom

cnv_prefilter

2

If we are using our own bed file with CNV calls(not using CNVKit), do we need to call cnv_prefilter or is using amplified_intervals.py enough? What additional filtering does cnv_prefilter do?

uretaj

Docker permissions

18

Just pulled PAA down the other day and have running it, my run command is: /data/PrepareAA/docker/run_paa_docker.py -o /data/output -s Colo -t 16 --bam /data/Data/Colo/cofinal.bam --run_AA --run_AC however after 22+ hours...

MrDotOne

Long run time with *_CNV_CALLS_pre_filtered.bed

4

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...

WeijiaSu

Suggestions for arguments to AA to tweak?

1

I have a few WGS samples (matched T/N) at 80X with relatively high purity and have matched FISH showing ecDNA with the target gene. I ran amplicon architect suite with...

tischfis

In most runs AA_CNV_SEEDS.bed files are empty

7

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...

Yumo-Xie