Posts
Transcriptome Annotation - Trinotate on C.bairdi Transcriptome v4.0 on Mox
Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from 20210317(https://robertslab.github.io/sams-notebook/2021/03/17/Transcriptome-Assembly-C.bairdi-Transcriptome-v4.0-Using-Trinity-on-Mox.html)] using Trinotate on Mox. This will provide a thorough annotation, including genoe ontology (GO) term assignments to each contig.
Transcriptome Annotation - DIAMOND BLASTx on C.bairdi Transcriptome v4.0 on Mox
Continued annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from 20210317(https://robertslab.github.io/sams-notebook/2021/03/17/Transcriptome-Assembly-C.bairdi-Transcriptome-v4.0-Using-Trinity-on-Mox.html)] using DIAMOND BLASTx on Mox. This will be used as a component of Trinotate annotation downstream.
TransDecoder - C.bairdi Transcriptome v4.0 on Mox
Began annotation of cbai_transcriptome_v4.0.fasta [Trinity de novo assembly from 20210317(https://robertslab.github.io/sams-notebook/2021/03/17/Transcriptome-Assembly-C.bairdi-Transcriptome-v4.0-Using-Trinity-on-Mox.html)] using TransDecoder on Mox. This will be used as a component of Trinotate annotation downstream.
Transcriptome Assessment - BUSCO Metazoa on C.bairdi Transcriptome v4.0 on Mox
I previously created a C.bairdi de novo transcriptome assembly v4.0 with Trinity from all our C.bairdi RNAseq reads which had BLASTx matches to the C.opilio genome and decided to assess its “completeness” using BUSCO and the metazoa_odb9 database.
Transcriptome Assembly - C.bairdi Transcriptome v4.0 Using Trinity on Mox
Continuing to addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I finally got to the point of actually running the assembly using Trinity using the extracted reads from 20210316. Those reads were identified via BLASTx agianst the C.opilio genome proteins on 20210312. Trinty was run on Mox.
Read Extractions - C.bairdi RNAseq Reads from C.opilio BLASTx Matches with seqkit on Mox
As part of addressing this GitHub issue, to generate an additional C.bairdi transcriptome, I needed to extract the reads ID’ed via BLASTX against the C.opilio genome on 20210312. Read extractions were performed using SeqKit on Mox.
DIAMOND BLASTx - C.bairdi RNAseq vs C.opilio Genome Proteins on Mox
We want to generate an additional Tanner crab (Chionoecetes bairdi) transcriptome, per this GitHub issue, to generate an additional C.bairdi transcriptome. This has come about due to the release of the genome of a very closely related crab species, Chionoecetes opilio (Snow crab).
Transcriptome Annotation - Trinotate Hematodinium v1.7 on Mox
Transcriptome Annotation - Trinotate Hematodinium v1.6 on Mox
Transcriptome Assembly - Hematodinium Transcriptomes v1.6 and v1.7 with Trinity on Mox
I’d previously assembled hemat_transcriptome_v1.0.fasta on 20200122, hemat_transcriptome_v1.5.fasta on 20200408, extracted hemat_transcriptome_v2.1.fasta from an existing FastA on 20200605, as well as extracted hemat_transcriptome_v3.1.fasta on 20200605.