Yellowhorn genome project

Best blast hit between yellowhron and other species

best_blast.sh

Expression

• mapping the rnaseq reads to genome using hisat2 and call count using htseq-count

  xso_gene_expr.sh

• convert the raw counts generated from htseq-count to vst using DEseq2

  convert_counts_to_VST.R

• remove non-varying genes

  vst_filter.R

• Calculate co-expression network using Seidr

  • Infer: Independent gene-gene networks are created by 12 algorithms

    seidr_algorithms.sh

  • Import: In order to merge these networks, they are first sorted and ranked

    seidr_import.sh

  • Aggregate: Once all methods are ready, seidr can aggregate them to a crowd network

    seidr_aggregate.sh

  • Estimate a hard threshold for a given seidr network

    seidr_threshold.sh

  • Construct the backbone network

    backbone.sh

  • Compare the backbone network and threshold network

    Two principles: (1) We would like to select the backbone network for further analysis. (2) The genes in the backbone network should contain the important genes (we determine whether the unique genes is important
    according to use the GO enrichment analysis) found in the threshold network as much as possible.

    compare.sh

  • run seidr roc for 'irp' aggregated network, backbone networks and threshold (irp, 0.28) network

    roc.sh

  • Visualisation and GO enrichment for the comparisons

    visualize_comparisons.sh

  • modules detection and annotated the modules suing GO enrichment

    modules_detection.sh

GO, PFAM and KEGG enrichment

enrichment_files.sh

Jbrowse

configure.sh

TF binding site prediction

Database

promoter.sh