User: babji2318

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babji23180
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Posts by babji2318

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Clusterprofiler with a set of GO Terms
... I work with a species that is not well annotated and hence I made a trinity assembly on my own and did the analysis. I am looking at a set of 1000 genes that I am interested in profiling. I did a local blast and annotated the genes using Blast2GO. Is there a way I can visualize a list in the format ...
go term visualization clusterprofiler gsea written 3 months ago by babji23180
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RNA-SEQ SNP calling
... I am comparing the effect of knocking down a gene in Aedes aegypti, I did a RNA-SEQ to understand expression profiles, I am also using this RNA-SEQ against the genome to check for variants I did a variant analysis using the GATK variant calling program, since GATK 4 doesnt support RNA-seq variant ca ...
indel variant snp rna-seq written 5 months ago by babji23180 • updated 5 months ago by JC8.0k
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Coverage Depth Transcriptome Assembly
... I am trying to estimate coverage depth for my de novo transcriptome assembly. I used Illumina Hiseq 3000/4000 PE with a PF yield of 140 million clusters. Since the organism hasn't been studied before I am having trouble finding the total number of transcripts. Can someone tell me of a way to calcul ...
assembly next-gen rna-seq written 9 months ago by babji23180

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