Part of the Pilon prep for polishing the PacBio Oly assembly is feeding it a bunch of Illumina data aligned to the PacBio assembly using your favorite aligner, in my case Bowtie2. I initially got a bunch of `.sam` files from Bowtie2 and wanted to convert them, so I turned to Google like any good person does these days. After looking at a bunch of different options, all answers pointed to `samtools view -sB file.sam > file.bam` as the preferred way to do this.
Thinking I knew what I was doing, I whipped up a quick slurm job script to convert everything and file up Pilon. It completed in less than 5 minutes, with a bunch of `.bam` files ~40kb in size. This was suspect, as their original `.sam` files were ~40gb.
After a reading the samtools manual, which corroborated the above conversion syntax, re-aligning some of the Illumina data files thinking I’d done something wrong there, and a whole bunch more googling, it turns out the `> file.bam` syntax is actually supposed to be `-o file.bam`.
Apparently the internet and documentation does not keep up with program changes as well as we’d like.
Finished the Pilon prep (except for .sam -> .bam conversion) yesterday afternoon. Found a 32-35% mapping rate for Illumina sequencing files to the PacBio backbone. Not great, but hopefully the whole meta-assembly route will manage to combine everything together in to one super assembly.
For fun, I mapped an Illumina file to a couple of the BGI assemblies, and got ~75% mapping. Wish we could have gotten that out of the PacBio thing, but ah well.
Im transferring the .sam files over to Owl now, but they’re ~40gb a piece, so that’ll take a bit. Will update here when finished!
Went in to UW to continue imaging Laura’s slides. Imaged slides 3-10. Here are the samples that I either couldn’t find gonad tissue in or I wasn’t quite sure about:
Oly 3 slide: HL-6_13 (not sure if I captured gonad tissue), HL-6_14 (none, no picture)
Oly 6 slide: NF-6_17 (none, no picture), NF-6_19 (not sure if I captured gonad tissue)
Oly 7 slide: NF-6_18 (not sure if I captured gonad tissue)
Oly 8 slide: SN-6_18 (not sure if I captured gonad tissue)
I will go through all of my noted questionable slides when I’m done.