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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
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WARNING: 5355 reads with length < 80: this program is designed for long reads. #39

Closed HelloYiHan closed 7 years ago

HelloYiHan commented 7 years ago

Hello Brent,

I make simulation fastq files and then use bwa-meth to calculate methylation rate. First, i simulate RRBS reads. Second, i trim those RRBS reads using trim_galore. Then i use bwa-meth to calculate the methylation rate. But after running bwameth.py, it says

WARNING: 5355 reads with length < 80 : this program is designed for long reads

Could you be kind enough to help me solve this problem ?

Thanks

brentp commented 7 years ago

that's just a warning. you should still have output, but bwa-meth uses bwa mem which is best on long reads.

HelloYiHan commented 7 years ago

Yes, i have an .bam output. But when i use pileOMeth, i get .bedGraph file. The file says

track type="bedGraph" description="pileometh.sample20360.result CpG methylation levels"