Posts
Daily Bits - October 2022
Data Wrangling - C.virginica NCBI GCF_002022765.2 GFF to Gene and Pseudogene Combined BED File
Working on the CEABIGR project, I was preparing to make a gene expression file to use in CIRCOS (GitHub Issue) when I realized that the Ballgown gene expression file (CSV; GitHub) had more genes than the C.virginica genes BED file we were using. After some sleuthing, I discovered that the discrepancy was caused by the lack of pseudogenes in the genes BED file I was using. Although it might not really have any impact on things, I thought it would still be prudent to have a BED file that completely matched all of the genes in the Ballgown gene expression file. Plus, having the pseudogenes might be of longterm usefulness if we we ever decide to evalute the role of long non-coding RNAs (lncRNAs) in this project.
BSseq SNP Analysis - Nextflow EpiDiverse SNP Pipeline for C.virginica CEABIGR BSseq data
Steven asked that I identify SNPs from our C.virginica CEABIGR BSseq data (GitHub Issue). So, I ran sorted, deduplicated Bismark BAMs that Steven generated through the EpiDiverse/snp Nextflow pipeline. The job was run on Mox.
Data Wrangling - Identify C.virginica Genes with Different Predominant Isoforms for CEABIGR
During today’s discussion, Yaamini recommended we generate a list of genes with different predominant isoforms between females and males, while also adding a column with a binary indicator (e.g. 0 or 1) to mark those genes which were not different (0) or were different (1) between sexes. Steven had already generated files identifying predominant isoforms in each sex:
RNAseq Alignments - P.generosa Alignments and Alternative Transcript Identification Using Hisat2 and StringTie on Mox
As part of identifying long non-coding RNA (lncRNA) in Pacific geoduck(GitHub Issue), one of the first things that I wanted to do was to gather all of our geoduck RNAseq data and align it to our geoduck genome. In addition to the alignments, some of the examples I’ve been following have also utilized expression levels as one aspect of the lncRNA selection criteria, so I figured I’d get this info as well.
FastQ Trimming - Geoduck RNAseq Data Using fastp on Mox
Per this GitHub Issue, Steven asked me to identify long non-coding RNA (lncRNA) in geoduck. The first step is to aggregate all of our Panopea generosa (Pacific geoduck) RNAseq data and get it all trimmed. After that, align it to the genome, followed by Ballgown expression analysis, and then followed by a variety of selection criteria to parse out lncRNAs.
Daily Bits - September 2022
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FastQ Trimming and QC - C.virginica Larval BS-seq Data from Lotterhos Lab and Part of CEABIGR Project Using fastp on Mox
We had some old Crassostrea virginica (Eastern oyster) larval/zygote BS-seq data from the Lotterhos Lab that’s part of the CEABiGR Workshop/Project (GitHub Repo) and Steven asked that I QC/trim it in this GitHub Issue.
Data Wrangling - Convert S.namaycush NCBI GFF to genes-only BED file for Use in Ballgown Analysis
In preparation for isoform identificaiton/quantification in S.namaycush RNAseq data, Ballgown will need a genes-only BED file. To generate, I used GFFutils to extract only genes from the NCBI GFF: GCF_016432855.1_SaNama_1.0_genomic.gff. All code was documented in the following Jupyter Notebook.
Splice Site Identification - S.namaycush Liver Parasitized and Non-Parasitized SRA RNAseq Using Hisat2-Stingtie with Genome GCF_016432855.1
After previously downloading/trimming/QCing S.namaycush SRA liver RNAseq data on 20220706, Steven asked that I run through Hisat2 for splice site identification (GitHub Issue).