Fastq polishing
DakeshiKitano opened this issue · 1 comments
DakeshiKitano commented
Dear developers,
I am glad and thankful for your tool for Hi-C Data Analysis! I have a question regarding the beginning of the analyses.
Do I need to process my .fastq files to remove the reads of low quality (low q30), or to remove duplicates? Or can I align with .fa genome file (e.g. mm39.fa) straightforward to generate .bam file with "samtools"?
hicexplorer 3.7.2, Python 3.10.13, conda 4.12.0
joachimwolff commented
Low quality will be filtered out in the build process of the interaction matrix, parameter minMappingQuality is used to set the level.