gonzalezlab/chimerics-transcripts-dmelanogaster

Scripts and data for the paper "Transposons contribute to the diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains".

Chimeric gene-TE transcripts in D. melanogaster natural strains

Scripts and data for the paper "Transposons contribute to the diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains".

Directories

• Chimeric gene-TE transcripts: folder that contains a tsv file with the 1,931 chimeric transcripts reported
• Reference-guided transcriptome assembly: contains the script to perform the reference-guided transcriptome assembly following Pertea et al. 2016
• Detection of chimeric genes: De novo transcriptome assembly, RepeatMasker and Minimap2: contains the scripts to perform the de novo transcriptome assembly using Trinity, and run RepeatMasker on the de novo transcripts and align the transcript to the genome with Minimap2. Also contains TRF script.
• Splice sites motifs: scripts using the MEME suite to find the splice sites motif in D. melanogaster exon-intron junctions
• ChIP-seq encode pipeline: a sample script to run the encode pipeline (mapping and peak calling)
• CPAT: script to run CPAT
• pfamScan: script to run PFAM
• Roo analyses: scripts to perform the blast analysis with the roo region
• GO clustering: script to parse GO clustering David tool output
• Rmd: Rmd document to reproduce all analyses and figures of the paper

Citation

Coronado-Zamora & González (2023) Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains. Genome Research gr.277565.122.

Contact

Project: https://github.com/GonzalezLab/chimerics-transcripts-dmelanogaster

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