icebert / eccdna_rca_nanopore Goto Github PK

Hi eccDNA_RCA_nanopore team,

Thanks for developing such an useful tool. I might have a general question about two empty output files. First, in the sequence info file, the values for all columns are zero, including Nfullpass, Nfragment, refLength, seqLength, and fragments. Second, the variant call file is also empty. I am wondering if you have any clue of what caused this problem?

Thank you in advance!
Yue

Hello,
I have a question while understanding the code, at line 333 of eccDNA_RCA_nanopore.py

When looping, when a fragment is unqualified, all subsequent fragments including it will be filtered out, instead of only this one fragment, why is this?

Traceback (most recent call last):
  File "./software/eccDNA_RCA_nanopore/eccDNA_RCA_nanopore.py", line 577, in <module>
    cs = ConsensusSequence(fastq, genome, read).callConsensus()
  File "./software/eccDNA_RCA_nanopore/eccDNA_RCA_nanopore.py", line 525, in callConsensus
    consensus[i].align(seq, readInterval, refInterval, frag.cigar)
  File "./software/eccDNA_RCA_nanopore/eccDNA_RCA_nanopore.py", line 440, in align
    self.sequence[ref_cur-1].insert(seq[read_cur:read_cur+step])
  File "./software/eccDNA_RCA_nanopore/eccDNA_RCA_nanopore.py", line 381, in insert
    self.nt[self.last] -= 1
KeyError: ''

Hi, I met an error like this, do you know why ?

Hi, Excuse me, what are the formats of the three files output by eccDNA_RCA_nanopore?
Are there any output instructions?

thanks！

Hi meng,
I'm wondering why trim adapter with porechop after Guppy trim barcode? BC and adapter has removed after guppy.

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 running eccDNA_RCA_nanopore, the data from the info file (fullpass1 reads, unique eccDNA) differs from the results reported in the article.

command:
porechop -i SRR13602435.fastq -o trim.fastq --extra_end_trim 0 --discard_middle
/minimap2-2.17/minimap2 -cx map-ont mm10.combined.fa SRR13602435.fastq -t 16 --secondary=no >mapping.paf
python eccDNA_RCA_nanopore.py --fastq SRR13602435.fastq --paf mapping.paf --reference mm10.combined.fa --info info --seq seq --var var --verbose --minDP 4 --minAF 0.75 --maxOffset 20 --minMapQual 30 |tee out.log

fullpass1 reads: less info |awk '$2>=1'|wc -l
unique eccDNA: less info |awk '$2>=2'|cut -f 6|sort|uniq|wc -l

What could this issue be?

Hello,
I was trying to run the pipeline with my eccDNA data. I got some confusing results. My reference (>MLV) is 8857bp, however, in the output, some fragments are longer than the reference.

For example:
f75c8bb0-38ca-4579-b1e6-a45a51d4d258 4 1 2053 735 MLV:8123-10175(+)
684c27d0-97bf-4900-b2a0-9ca1991625e4 2 1 2823 1362 MLV:7496-10318(+)

I also got some results with coordinates <0

For example:
de744270-bb0d-40a9-9763-a3e37f0aabb4 4 2 2789 140 MLV:3034-3173(-)|MLV:-1115-1533(+)

Any suggestions would be appreciated.

Thanks
Weijia