I am running Bisulfide sequencing samples. I've directional libraries with four single-ended fastq files for each sample and completed with bismark and got four bam files which i've merged and finally got one bam file for each sample.
These are the commands I ran:
bismark --genome_folder /home/xyz/mm10 read1.fastq,read2.fastq,read3.fastq,read4.fastq -o /home/out/ --parallel 3 -p 10 --temp_dir /home/tmp_dir/ samtools merge out.bam read1.bam read2.bam read3.bam read4.bam bismark_methylation_extractor --bedGraph -o /home/out/ out.bam bismark2report bismark2summary bam2nuc --genome_folder /home/xyz/mm10 out.bam --dir /home/out/
I have got around 26 output files. now I want to analyse outputs with RnBeads R package, but I'm not able to import bismark result to RnBeads. Please suggest which bismark output file I should use for RnBeads.
Thanks in advance!! Any help appreciated!!