I tried to do some bisulfite alignment with some data sample from internet. I chose bismark for alignment and methylation call. After I ran the process for several sample, the result is strange. It seems it failed to do the alignment because in the text file from bismark, there is only 1 or 0 values for the methylation detected, unmethylation, and coverage. So, I think it's because I use the wrong human genome reference. I download the reference from this site :
I dowload hg38.fa.gz and use it for bowtie indexing. Because of that, I think maybe I use the wrong file for bowtie indexing. Is there any advice which file I use?
I use trim_galore to trim the data and use FastQC to check the quality before and after the trimming process.
Bismark version 0.14 (just download it from the website)
Use bowtie (not bowtie2, because it said bowtie is good for shorter reads, mine is shor read, 46 bp)
Command I use :
To build the genome rindex :
bismark_genome_preparation <folder> (I already set every executable in the environment variable)
To call the methylation data :
bismark -n l -l 50 <reference> <file fastq>
bismark_methylation_extractor -s --comprehensive <file .sam>
Thank you very much for your help.