What do to after converting Bam file to uBam or Fastq file

Question

[williamsbrian5064]

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

Answer 1

[h.mon]

You cram too many questions into one post. I wil answer them randomly for added fun.

I am not sure if this uBam file would be considered "single-end" if it is only one file?

If the original fastq / bam files were from paired-end sequencing, the uBam will contain paired-end sequencing.

I was curious if this is the best method?

If you plan to use GATK down the road, this us probably the best method. If you plan to do something else, it is probably a good method, though not necessarily the best.

can you still trim a uBam file with trimmomatic?

I really don't know if Trimmomatic accepts uBam (I guess it doesn't), you should read its documentation. But if the data has already been trimmed, why would you want to trim it again?

After I revert back to a uBam file, do you align with bwa mem still?

You can align with your aligner of choice, but typically converting / streaming ubam to fastq. BWA does not accept uBam as input.

[williamsbrian5064]

"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!