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Daily Log
Karthik Nair edited this page Sep 6, 2019
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Finished read quality assessment using FastQC. Used Trimmomatic to trim files
Genome Assembly using SPAdes, GapCloser, SOAPdenovo.
SOAPdenovo and SPAdes completed
Trinity run for paired reads. Unpaired giving errors. Evening Update: Trinity paired reads finished.
Used MUMmer + Nucmer for Assembly validation. Used Quast on local machine.
Annotation using Maker2 on Sopadenovo results with sel3 data. SNAP, Augustus training done. Maker run finished.
Bowtie and Tophat finished.
HTSeq completed. CS17 hindlimb causing errors. Afternoon Update: Errors couldn't be fixed. Removal of cs17 hindlimb set worked. Genes identified using bash script for blast. Evening update: Deseq2 completed locally.