Pore-C-Snakemake
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nanoporetech
When running the pipeline using the test data, I encountered the below error. Could you please help me figure out how to solve this issue? (Until step 5 pipeline ran...
Hi, While running the pipeline on the test data, I keep getting an error concerning the haplotag rule (all previous jobs excited successfully): ``` (pore-c-snakemake) [vsc42297@gligar05 Pore-C-Snakemake]$ snakemake --use-conda --cluster...
Hi! I am getting an error with the penultimate step of the Snakemake workflow: ``` pore_c --dask-scheduler-port 0 --dask-num-workers 4 contacts summarize AF_porec/merged_contacts/HhaI_run01_genome.2_unphased.contacts.parquet AF_porec/basecall/HhaI_run01.rd.summary.csv AF_porec/merged_contacts/HhaI_run01_genome.2_unphased.concatemers.parquet AF_porec/merged_contacts/HhaI_run01_genome.2_unphased.concatemer_summary.csv --user-metadata '{"run_id":"run01","enzyme":"HhaI","biospecimen":"lab","refgenome_id":"genome.2","phase_set_id":"unphased"}' ``` ```...
From the community post (https://community.nanoporetech.com/posts/assembly-of-oryza-sativa), I noticed that in Fig. 1 Pore-C could produce pseudo paired-end fastq after generating the contact map. I wonder if this function still exists? I...
Hello Eoghan and Team, in your Pore-C Snakemake pipeline you are providing a nice contact summary file including the total numbers and percentage of short and long range cis-contacts, respectively....
Hi Eoghan Just a clarification question. I was parsing through the alignment stat output at logs/results/merged_contacts/*.concatemers.parquet.log and saw direct vs. indirect contact numbers. I went back the pore-c biorxiv and...
Can I get the list of actual commands that are used to run this pipeline? I have been growing increasingly frustrated by this snakemake implementation. Some jobs are aborted with...
Hello. (edited for clarity) I was wondering if it is possible to specify the mapq threshold for read filtering in pore-c-snakemake. Now, I have to calculate all those stats (contacts...
I found that the pipeline was failing when downloading juicer_tools. Since the log file was empty, I figured I run the wget commant myself. The error I found is "no...
Hello Eoghan and team, After multiple rounds of nanopore sequencing we have reached to 50-60 Gbases data for each sample. Pore-C run results in ~250 million contacts each. However downstream...
