Closed kekaiko closed 11 months ago
Hi hisat-3n developers,
Thank you for building this wonderful aligner!
I use hisat-3n to align my WGBS data with code : hisat-3n --index $Index_filename_prefix \ -q -1 $trim_read1 -2 $trim_read2 \ --base-change C,T \ --sensitive \ --threads 40 \ --no-spliced-alignment \ --time --met 3 \ --repeat \ --new-summary --summary-file "$summary_file" \ --directional-mapping-reverse | ~/anaconda3/envs/WGBS/bin/samtools view -@ 40 -b -q 10 -o $bam_file
hisat-3n --index $Index_filename_prefix \ -q -1 $trim_read1 -2 $trim_read2 \ --base-change C,T \ --sensitive \ --threads 40 \ --no-spliced-alignment \ --time --met 3 \ --repeat \ --new-summary --summary-file "$summary_file" \ --directional-mapping-reverse | ~/anaconda3/envs/WGBS/bin/samtools view -@ 40 -b -q 10 -o $bam_file
Then the outputs are removing duplication by sambamba.
After that I use MethylDackel to extract my methylation information with parameter： --fraction.
Curiously, The methylation percentage is almost 100%.
My guess is it has to do with the "--directional-mapping-reverse".
Do you any suggestions? Best wishes
Hi hisat-3n developers,
Thank you for building this wonderful aligner!
I use hisat-3n to align my WGBS data with code :
hisat-3n --index $Index_filename_prefix \ -q -1 $trim_read1 -2 $trim_read2 \ --base-change C,T \ --sensitive \ --threads 40 \ --no-spliced-alignment \ --time --met 3 \ --repeat \ --new-summary --summary-file "$summary_file" \ --directional-mapping-reverse | ~/anaconda3/envs/WGBS/bin/samtools view -@ 40 -b -q 10 -o $bam_fileThen the outputs are removing duplication by sambamba.
After that I use MethylDackel to extract my methylation information with parameter： --fraction.
Curiously, The methylation percentage is almost 100%.
My guess is it has to do with the "--directional-mapping-reverse".
Do you any suggestions? Best wishes