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00_Files.md

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Files generate for this project and their location

Raw data location

#ceres
/lustre/project/elk_bison_genomics/rawdata/elk/mRNA/3_4_22061_Elk-muscle_HVW3J_1422.tar

Illumina Reads

#ceres
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/1_9130_01_WY1-Pine_HF557_1013.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/1_9138_01_2510-Os-Mn_HH7YG_1052.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/2_9131_01_WY2-Pine_HF557_1013.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/2_9139_01_2486-OS-Mn_HG73W_1014.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/3_9132_01_WY3-Pine_HF557_1013.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/3_9140_01_2758-OS-Mn_HG73W_1014.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/4_9133_01_WY7-Pine_HF557_1013.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/4_9141_01_2763-OS-Mn_HG73W_1014.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/5_9134_01_WY8-Pine_HF557_1013.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/5_9142_01_8Bull-OSMn_HG73W_1014.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/6_9135_01_WY10-Pine_HF557_1013.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/6_9143_01_8Bull-OSMn_HG73W_1014.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/7_9136_01_2458-0S-Mn_HF557_1013.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/7_9144_01_8Bull-OSMn_HG73W_1014.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/8_9137_01_2450-OS-Mn_HF557_1013.tar
/lustre/project/elk_bison_genomics/rawdata/elk/illumina/8_9145_01_8Bull-OSMn_HG73W_1014.tar

Nanopore Reads

Pacbio Reads

/lustre/project/elk_bison_genomics/rawdata/elk/pacbio/10_9649_Bull-Elk1_PacBio_1060_1.tar.bz2
/lustre/project/elk_bison_genomics/rawdata/elk/pacbio/10_9649_Bull-Elk1_PacBio_1060.tar.bz2
/lustre/project/elk_bison_genomics/rawdata/elk/pacbio/10_9650_Bull-Elk2_PacBio_1061_1.tar.bz2
/lustre/project/elk_bison_genomics/rawdata/elk/pacbio/10_9650_Bull-Elk2_PacBio_1061_2.tar.bz2
/lustre/project/elk_bison_genomics/rawdata/elk/pacbio/10_9650_Bull-Elk2_PacBio_1061.tar.bz2
/lustre/project/elk_bison_genomics/rawdata/elk/pacbio/10_9651_Bull-Elk3_PacBio_1067.tar.bz2
/lustre/project/elk_bison_genomics/rawdata/elk/pacbio/10_9651_Bull-Elk3_PacBio_1078.tar.bz2
/lustre/project/elk_bison_genomics/rawdata/elk/pacbio/10_9652_Bull-Elk4_PacBio_1079.tar.bz2

Hi-C data

#ceres
/lustre/project/elk_bison_genomics/rawdata/elk/dovetail

SNP data

RNA-Seq data

Genome Assembly

#nova
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/CervusCanadensisGenome.fa.gz
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/CervusCanadensisGenome.fa.fai

Genome Annotation

#nova
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/FinalHighConfidenceGenes.gff3.gz
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/FinalHighConfidenceGenes.gff3.gz.tbi

/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/FinalHighConfidenceGenes_transcripts.fasta
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/FinalHighConfidenceGenes_proteins.fasta

SNP data

Final Files of Importance

repeat prediction

#nova
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/EDTATransposons.gff.gz
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/EDTATransposons.gff.gz.tbi

/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/Repeatmasker.gff3.gz
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/Repeatmasker.gff3.gz.tbi

#genes annotated as transposons
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/ExpressedTransposableElements.gff3.gz
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/ExpressedTransposableElements.gff3.gz.tbi

#genes that overlap with a repeat track
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/GenesWithRepetitiveOverlap.gff3.gz
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/GenesWithRepetitiveOverlap.gff3.gz.tbi

Low confidence genes

#nova
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/LowConfidenceGenes.gff3.gz
/work/gif/remkv6/Olsen/Elk/08_RenameAgain/01_Move2Box/LowConfidenceGenes.gff3.gz.tbi