I’m a genomic newbie, so I believe my question is a basic one.
I need to transform raw fastq files into plink .bed files. From my biostar searchers it appears I cannot directly transform fastq sequence files to a .bed format, as I would first need to first transform the fastq to .bam files. It appears after I generate .bam files I can then convert these .bam to plink .bed files?
• Which tools (i.e. galaxy, etc) are best to convert fastq to .bam
• Which tools (i.e. bedTools) can be used to convert .bam to plink .bed
Any additional information regarding these format "conversions" would be helpful. I had difficulty installing Bowtie.