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how to acquire or calculate the mapping efficiency using methylpy? #82
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it is in the output file. For example:
|
Thank you so much for your answer. May i ask is there any way to output these information to a certain file like Bismark. For I have many sample to analyze, and currently these information were output to one file named |
Yes you can do something like |
Hello, as a new learner of methylpy I am curious about how to acquire mapping efficiency, since it seems not shown in the output result in total. I used to use bismark, and the mapping efficiency is about 40-60%, which is quite low when compared with other plant species. I have looked through bowtie2 report but it seems different from this.
Therefore i try to replace it this methylpy.
my code is as follows:
methylpy paired-end-pipeline --read1-files ../samplename_clean.1.fq.gz --read2-files ../samplename_clean.2.fq.gz --sample samplename --forward-ref ../methypy_ref/genome_f --reverse-ref ../methypy_ref/genome_r --ref-fasta ../fasta --num-procs 20 --trim-reads False --compress-output True --remove-clonal True --path-to-picard /direction_to_picard/software/
my result report is as follows:
Bismark result is as follows:
Thank you and looking forward to the anawer.
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