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rki-mf1 / CoVpipe2

SARS-CoV-2 genome reconstruction for Illumina data in Nextflow
GNU General Public License v3.0
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primer clipping for polio virus #66

Closed NmnBttr closed 8 months ago

NmnBttr commented 1 year ago

First of all thank you for this great pipeline. I am currently trying to apply CoVpipe2 on Polio virus data. After adjusting the input data I was able to run the pipeline. The results came out good with all the output files, plots and reports, however the primer clipping seems to not work. I searched the primer sequences in both clipped and non clipped files and they still had the primer sequences. Can you please help me with this issue?

For reproducing I included a reference fasta file, primer bed file and a tsv file with the primer sequences. In case a fastq file is needed it can be shared through other channels. Polio1.tar.gz

This is how the pipeline was called

nextflow run rki-mf1/CoVpipe2 --ref_genome $REF --fastq $WORK_DIR/samplesheet.csv --list --cores 4 --max_cores 8 -r v0.4.2 -profile local,docker --primer_bed $PRIMER

Thank you in advance!

MarieLataretu commented 1 year ago

Hi @NmnBttr ,

cool nice to hear! As I understand the pipeline run successfully without errors, correct?

Do you have by chance a IGV screenshot (shared through other channels if sensitive)? Or how did you search for the primer sequences in the BAM files directly?

NmnBttr commented 1 year ago

Hi @MarieLataretu,

thank you for the quick reply! Yes the pipeline runs without any error. I can share you an IGV screenshot through email if that's okay. I also searched for the primer sequences not in the bam files directly but I converted them using samtools into fastq files then I used grep to search for the primer sequences.

hoelzer commented 8 months ago

This can be closed: the primer BED file was not correctly adjusted to the used reference and thus the primer clipping probably failed.

Here is a script now in case someone has a primer BED that is not matching the used reference and needs adjustment first:

https://github.com/rki-mf1/update-varvamp-bed