Posts
Samples Submitted - M.magister MBD-BSseq Libraries to Univ. of Oregon GC3F
Submitted the M.magister MBD-BSseq libraries created 20201124 using the 4nM aliquots created for the MiSeq test run on 20201202 to the Univ. of Oregon GC3F sequencing core.
Transcriptome Comparisons - C.bairdi Transcriptomes Evaluations with DETONATE rsem-eval on Mox
UPDATE: I’ll lead in with the fact that this failed with an error message that I can’t figure out. This will save the reader some time. I’ve posted the problem as an Issue on the DETONATE GitHub repo, however it’s clear that this software is no longer maintained, as the repo hasn’t been updated in >3yrs; even lacking responses to Issues that are that old.
Alignments - C.bairdi RNAseq Transcriptome Alignments Using Bowtie2 on Mox
I had previously attempted to compare all of our C.bairdi transcriptome assemblies using DETONATE on 20200601, but, due to hitting time limits on Mox, failed to successfully get the analysis to complete. I realized that the limiting factor was performing FastQ alignments, so I decided to run this step independently to see if I could at least get that step resolved. DETONATE (rsem-eval) will accept BAM files as input, so I’m hoping I can power through this alignment step and then provided DETONATE (rsem-eval) with the BAM files.
Samples Received - Cockle Clam Gonad H and E Slides
Today we received the H & E-stained slides from the cockle clam gonad tissue blocks/cassettes we submitted on 20201201. Slides were added to Slide Case #5 - Rows 13 - 37 (Google Sheet).
FastQC-MultiQC - M.magister MBD-BSseq Pool Test MiSeq Run on Mox
Earlier today we received the M.magister (C.magister; Dungeness crab) MiSeq data from Mac.
Data Received - M.magister MBD-BSseq Pool Test MiSeq Run
After creating _M.magister (C.magister; Dungeness crab) MBD-BSseq libraries (on 20201124), I gave the pooled set of samples to Mac for a test sequencing run on the MiSeq on 20201202.
Alignment - C.gigas RNAseq to GCF_000297895.1_oyster_v9 Genome Using STAR on Mox
Mac was getting some weird results when mapping some single cell RNAseq data to the C.gigas mitochondrial (mt) genome that she had, so she asked for some help mapping other C.gigas RNAseq data (GitHub Issue) to the C.gigas mt genome to see if someone else would get similar results.
SRA Submission - Haws Lab C.gigas Ploidy pH WGBS
Trimming - Haws Lab C.gigas Ploidy pH WGBS 10bp 5 and 3 Prime Ends Using fastp and MultiQC on Mox
Making the assumption that the 24 C.gigas ploidy pH WGBS data we receved 20201205 will be analyzed using Bismark, I decided to go ahead and trim the files according to Bismark guidelines for libraries made with the ZymoResearch Pico MethylSeq Kit.
FastQC-MultiQc - C.gigas Ploidy pH WGBS Raw Sequence Data from Haws Lab on Mox
Yesterday (20201205), we received the whole genome bisulfite sequencing (WGBS) data back from ZymoResearch from the 24 C.gigas diploid/triploid subjected to two different pH treatments (received from the Haws’ Lab on 20200820 that we submitted to ZymoResearch on 20200824. As part of our standard sequencing data receipt pipeline, I needed to generate FastQC files for each sample.