Posts
Transdecoder - Hematodinium MEGAN6 Taxonomic-Specific Reads Assembly from 20200330
Ran Trinity to de novo assembly on the the Alveolata MEGAN6 taxonomic-specific RNAseq data on 20120330 and now will begin annotating the transcriptome using TransDecoder on Mox.
Transcriptome Assessment - BUSCO Metazoa on C.bairdi MEGAN Transcriptome
I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Arthropoda on 20200330 and decided to assess its “completeness” using BUSCO and the metazoa_odb9 database.
Transcriptome Annotation - Hematodinium MEGAN Trinity Assembly Using DIAMOND BLASTx on Mox
As part of annotating the most recent transcriptome assembly from the MEGAN6 Hematodinium taxonomic-specific reads, I need to run DIAMOND BLASTx to use with Trinotate.
Transcriptome Assessment - BUSCO Metazoa on Hematodinium MEGAN Transcriptome
I previously created a C.bairdi de novo transcriptome assembly with Trinity from the MEGAN6 taxonomic-specific reads for Alveolata on 20200331 and decided to assess its “completeness” using BUSCO and the metazoa_odb9 database.
Transcriptome Assembly - Hematodinium with MEGAN6 Taxonomy-specific Reads with Trinity on Mox
Ran a de novo assembly using the extracted reads classified under Alveolata from:
Transcriptome Assembly - C.bairdi with MEGAN6 Taxonomy-specific Reads with Trinity on Mox
Ran a de novo assembly using the extracted reads classified under Arthropoda from:
RNAseq Reads Extractions - C.bairdi Taxonomic Reads Extractions with MEGAN6 on swoose
Transcriptome Annotation - C.bairdi Using DIAMOND BLASTx on Mox and MEGAN6 Meganizer on swoose
After receiving/trimming the latest round of C.bairdi RNAseq data on 20200318, need to get the data ready to perform taxonomic selection of sequencing reads. To do this, I first need to run DIAMOND BLASTx, then “meganize” the output files in preparation for loading into MEGAN6, which will allow for taxonomic-specific read separation.
Trimming/FastQC/MultiQC - C.bairdi RNAseq FastQ with fastp on Mox
After receiving our RNAseq data from Genewiz earlier today, needed to run FastQC, trim, check trimmed reads with FastQC.
Data Received - C.bairdi RNAseq Data from Genewiz
We received the RNAseq data from the RNA that was sent out by Grace on 20200212.