Computer programs

  Homepage of the team

 GitHub repository

Manuscript “Pinzón et al., 2019”

Predicted animal proteome sequence download

Search for RdRP candidates and re-sequencing of the "BL09445" locuslocus “BL09945”

Phylogeny of the "eukaryotic RdRP" protein family

Small RNA-Seq in Branchiostoma lanceolatum

Filename Size
A file of unknown type 03_Small_RNA-Seq.md 29.47 KB
A Compressed file B_lanceolatum_genome_bowtie2_index.tar.bz2 776.93 MB
A Compressed file B_lanceolatum_transcriptome_bowtie2_index.tar.bz2 152.04 MB
A Compressed file Bl71nemr.fa.bz2 128.94 MB
A file of unknown type Chef3.sh 2.67 KB
A file of unknown type Chef4.sh 2.92 KB
A file of unknown type Convincing_pre-miRNA_hairpins.fa 6.26 KB
A file of unknown type Fuses_lines_clean.pl 514 bytes
An Adobe Acrobat file Gel_purification_8h_embryos.pdf 9.57 MB
An Adobe Acrobat file Gel_purification_15h_embryos.pdf 9.6 MB
An Adobe Acrobat file Gel_purification_36h_embryos.pdf 11.19 MB
An Adobe Acrobat file Gel_purification_60h_embryos.pdf 10.16 MB
An Adobe Acrobat file Gel_purification_adult_females.pdf 9.09 MB
An Adobe Acrobat file Gel_purification_adult_males.pdf 8.48 MB
A file of unknown type Junction_and_exonic_reads_blat_output.dat 172.2 KB
A file of unknown type Module_ORF_detector.pl 2.01 KB
A file of unknown type Module_ORF_detector_lower_case.pl 2.04 KB
A file of unknown type Module_TXT_to_FA.pl 513 bytes
A file of unknown type Module_converts_fastq_to_fasta.pl 539 bytes
A file of unknown type Module_excludes_hairpin-matching_reads.pl 1.42 KB
A file of unknown type Module_extract_from_fasta.pl 572 bytes
A file of unknown type Module_extract_from_fastq.pl 671 bytes
A file of unknown type Module_extracts_fastq_read_identifiers.pl 349 bytes
A file of unknown type Module_extracts_miRNA_hairpins.pl 1.35 KB
A file of unknown type Module_extracts_read_sequences.pl 748 bytes
A file of unknown type Module_logo_for_hairpin-matching.pl 1.89 KB
A file of unknown type Module_selects_from_blat_results.pl 4.35 KB
A file of unknown type Module_unification.pl 1.7 KB
A file of unknown type Orthologs_to_known_hairpins.fa 3.29 MB
A file of unknown type R_commands_convincing_ORF-matching_reads 1.89 KB
A file of unknown type R_commands_genomic_non_ncRNA-matching_size_dist 1.36 KB
A file of unknown type R_commands_hairpin-matching_size_dist 1.76 KB
A file of unknown type R_commands_hairpin_read_profile 2.76 KB
A file of unknown type R_commands_plot_miRNAs_in_dvpt 1.91 KB
A file of unknown type R_commands_size_distribution_September2017 4.01 KB
A file of unknown type R_commands_transcriptome_non_hairpin-matching_size_dist 1.87 KB
A file of unknown type R_commands_worm_convincing_ORF-matching_size_dist 1.88 KB
A file of unknown type R_commands_worm_extragenomic_extratranscriptomic_size_dist 1.33 KB
A file of unknown type R_commands_worm_genomic_non_ncRNA-matching_size_dist 1.34 KB
A file of unknown type R_commands_worm_hairpin-matching_size_dist 1.74 KB
A file of unknown type R_commands_worm_transcriptome_non_hairpin-matching_size_dist 1.85 KB
A file of unknown type R_commands_worm_transcriptomic_extragenomic_size_dist 1.77 KB
A file of unknown type RdRP_template_loci.bed 168 bytes
A file of unknown type Script_C_elegans.sh 6.69 KB
A file of unknown type Script_convincing_transcriptome-matching_not_matching_ncRNA_or_hairpins.sh 315 bytes
A file of unknown type Script_mapping_extragenomic_on_RdRP_template_loci.sh 713 bytes
A file of unknown type Script_mapping_on_RdRP_template_loci.sh 1.03 KB
A file of unknown type Script_miRNAs_in_development.sh 5.38 KB
A file of unknown type Script_transcriptome-matching_not_matching_ncRNA_or_hairpins.sh 1.05 KB
A file of unknown type Statistics.dat 1.08 KB
A file of unknown type Top_antisense_junction_mapped_mRNAs.dat 0 bytes
A file of unknown type Top_sense_junction_mapped_mRNAs.dat 314 bytes
A Compressed file Transcripts_with_convicing_ORFs_in_Bla_annot_final_refTranscripts.fa.bz2 10.25 MB
A Compressed file Trimmed_fastq.tar 2.44 GB
A file of unknown type abundant_B_lanceolatum_ncRNAs.fa 521.74 KB
A Compressed file blanc_evm+_rn.fa.bz2 7.72 MB
A Compressed file blat_output.psl.bz2 657.3 MB
A file of unknown type cel_abundant_ncRNAs.fa 129.46 KB
A file of unknown type cel_hairpinMar18.fa 37.51 KB
A file of unknown type hairpinMar18.fa 5.85 MB
A Text file md5sum_Seitz.txt 3.6 KB
A file of unknown type miRNA_abundance_in_development.dat 7.08 KB
A file of unknown type unified1.fa 1.1 MB

Pathogen and potential pathogen-matching reads

Manuscript "Mockly and Seitz, 2019"

Manuscript "Pinzón et al., 2017":

Scripts and data for the preparation of all 6 figures:

Cytometry FCS file to text file conversion:

Conversion script (usage : ./read_FCS.py input.fcs output.txt) : python script.