-
I have a question regarding the differentiation between amplifications occurring on eccDNA and those on the linear genome. So if a gene "A" present on an eccDNA is shown by AC to have x copy number. I…
-
Hi,
my command:
python3 /tools/ecc_finder/ecc_finder.py map-ont /reference/mm10.pc.idx S.fastq.gz -r /reference/mm10.fa -t14 -o ./S -x S --min-cov 1 -l 100 --min-read 1
error:
Processing experimen…
-
Hi, I have read your impressive work "Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma Nat Genet (2020)." But I didn't find some explicit criteria to distinguish ecDNA…
-
```
Traceback (most recent call last):
File "./software/eccDNA_RCA_nanopore/eccDNA_RCA_nanopore.py", line 577, in
cs = ConsensusSequence(fastq, genome, read).callConsensus()
File "./softw…
-
Circle-Map is a very good algorithm and help me much.
I have a problem of searching principle:
Is it possible that the predicted eccDNA includes more than one eccDNA?
In other words, after re…
-
Hi njaupan,
Thank you for the tool. May I know--
1) If the tool is dedicated for eccDNA-seq or it can be used to identify eccDNAs from WGS data?
2) Can we use HiFi reads as well?
thank you!
-
I used porechop to process the SRR13602435.fastq file, but there were no changes in the resulting fastq file.
Then, I aligned the SRR13602435.fastq to mm10.combined.fa using minimap2 V2.17. After r…
-
Dear njaupan,
Is there an option in ecc_finder that allows users to specify the max length of eccDNA to detect? I wonder if I can use it to identify long eccDNA with the size of 1-3 Mb. Currently w…
-
Hi Inigo,
I know that you use `get_mate_intervals` to build realign intervals, and you will use all the soft-clipped/hard-clipped reads and discordant reads in this function. But we know that if so…
-
Hello there,
I have used Amplicon suite on one cohort and it detected eccDNA in 6 out of 23 samples. Next I wanted to try it on another cohort with tumor-normal paired fastq files, but I have not yet…