Hi,
I am trying to convert a aligned BAM file back to a uBAM or Fastq file. I was planning on using this GATK method link but I was curious if this is the best method? This aligned Bam file was generated awhile ago, so I was thinking I should maybe try trimming the data a bit. If I were to use the suggest method from GATK, can you still trim a uBam file with trimmomatic? After I revert back to a uBam file, do you align with bwa mem still? I guess I am a bit confused because I am not sure if this uBam file would be considered "single-end" if it is only one file? I guess you can't go to picart sortsam because it is a bam file.
Thanks for the help
"You cram too many questions into one post. I will answer them randomly for added fun." I didn't see this line until now and it is quite funny. Regardless, I appreciate the help!