RESULTSDIR is the directory that you want the CENSOR output to go inĮ.g.DIR is the directory where you put your combined tblastn+lastz results.Sometimes, other repeats are picked up instead. We want to see if our "L1 hits" are truly L1s, as deemed by CENSOR, and if our "BovB hits" are truly BovBs. SPECIES=Yarrowia.lipolytica ELEMENT=L1 LASTZFILE=/data/rc003/atma/horizontalTransfer/results/L1/lastzed/Yarrowia.lipolytica_GCF_000002525.2_ASM252v1_genomic.fna_Yarrowia.lipolytica_GCF_000002525.2_ASM252v1_genomic.fna_L1_ORFp.fasta_nucl_seqs.fasta_lastz.bed TBLASTNFILE=/data/rc003/atma/horizontalTransfer/results/L1/tblastned/Yarrowia.lipolytica_GCF_000002525.2_ASM252v1_genomic.fna_L1_ORFp.fasta_merged.bed GENOME=/data/rc003/atma/horizontalTransfer/genomes/fungi/Yarrowia.lipolytica/Yarrowia.lipolytica_GCF_000002525.2_ASM252v1_genomic.fna RESULTSDIR=/data/rc003/atma/horizontalTransfer/results/L1/combined sbatch combineHits.qġg) Use CENSOR to categorise all extracted nucleotide sequencesĬensorSequences.q will use CENSOR to check sequences against the RepBase library of known repeat sequences. Most genomes are given useless names like GCF_000002525.2_ASM252v1_genomic.fna.įor example, to rename fungal genome Yarrowia lipolytica: This will save you a lot of headaches later on. 1b) Append species name to each genome fasta file See Supplementary Table 1 for the source and assembly version of each genome used. All genomes were downloaded using wget, as recommended by NCBI ( ). Workflow 1) Extraction of L1 and BovB retrotransposons from genome data 1a) Download or acquire genomes of interestħ55 genomes were downloaded from public databases (UCSC and NCBI) four more were acquired from collaborators. LaTeX files for the Additional Files (Supp Tables and Figures) are provided in latex. Analysis scripts are provided in scripts. Intermediate files for each step can be found in results/L1, to help with troubleshooting. We recommend trying out the workflow below on this genome first. ![]() ![]() Some level of familiarity with computers and queuing systems (SLURM)Ī test genome (fungus Yarrowia lipolytica) has been placed in genomes/fungi/Yarrowia.lipolytica.CENSOR, which requires wu-blast and bioperl ( ).Dataset from: Horizontal transfer of BovB and L1 retrotransposons in eukaryotes. Ivancevic, Atma M, Kortschak, R Daniel, Bertozzi, Terry, & Adelson, David L. AdelaideBioinfo/horizontalTransfer: First release of horizontal transfer code (Version v1.0.0). Code used to infer and filter horizontal transfer events involving L1 and BovB retrotransposons in eukaryotes.Ītma M Ivancevic.
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