Nanopore_Pore_C_Tips
Description
This Documentation provides some tips for running Nanopore Pore C pipeline
Tips
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Required input files:
a) a merged fastq file for each sample
b) raw fast5 files stored in one directory for each sample
c) a sequencing_summary text file for each sample
d) reference genome fasta file. The "GRCh38.fasta.gz" file provided by the original pipeline is NOT a real fasta file.
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To run on cluster
a) the correct conda environment name is : conda activate pore-c-snakemake, NOT pore_c_snakemake as shown in the original repo.
b) allow more than 4G memory for running snakemake, otherwise some conda environment installation may fail.
c) log files are stored at: results/logs/results/
d) the workflow "pairs" and "cooler" are not included in the workflow "all". You need to run them additionally.
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Output
a) I don't see any of the below output files were generated as described in the original repo, with or withour phased vcf file:
matrix/
pairs/
assembly/
juicebox/
b) a extra step is needed to merged all splited bam files
c) the DNA contact information is stored in the file: merged_contacts/*.concatemers.parquet. Convert it to the csv format if needed.