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Please also find the genomes with GTF annotations and bowtie2 indexes for the same genome assemblies as before but in ENSEMBL format:
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Human:
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/work/ladunga/SHARED/human/grch38.p5/ensembl/
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-rw-r----- 1 sladunga ladunga 23 Apr 18 10:50 bt2index.err
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-rw-r----- 1 sladunga ladunga 12207 Apr 18 13:37 bt2index.out
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-rw-r----- 1 sladunga ladunga 986172011 Apr 18 12:13 grch38.p5_primary.1.bt2
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-rw-r----- 1 sladunga ladunga 736462272 Apr 18 12:13 grch38.p5_primary.2.bt2
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-rw-r----- 1 sladunga ladunga 11294 Apr 18 10:52 grch38.p5_primary.3.bt2
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-rw-r----- 1 sladunga ladunga 736462267 Apr 18 10:52 grch38.p5_primary.4.bt2
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-rw-r----- 1 sladunga ladunga 986172011 Apr 18 13:37 grch38.p5_primary.rev.1.bt2
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-rw-r----- 1 sladunga ladunga 736462272 Apr 18 13:37 grch38.p5_primary.rev.2.bt2
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-rw-r----- 1 sladunga ladunga 51158 Apr 18 11:47 hg38_wgEncodeDacMapabilityConsensusExcludable.bed # This is the NEW hg38 genome’s blacklists
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-rwxrwxr-x 1 sladunga ladunga 1402361916 Mar 8 23:53 Homo_sapiens.GRCh38.84.gtf
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-rw-r--r-- 1 sladunga ladunga 3151425857 Feb 25 02:27 Homo_sapiens.GRCh38.dna.primary_assembly.fa
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-rw-r----- 1 sladunga ladunga 18786 May 4 2011 wgEncodeDacMapabilityConsensusExcludable.bed # This is the OLD hg19 genome’s blacklists
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Mouse:
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/work/ladunga/SHARED/mouse/GRCm38.p4/ensembl
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[sladunga@login:ensembl>l
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total 7266384
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lrwxrwxrwx 1 sladunga ladunga 57 Apr 18 11:21 bowtie2indexmouse.slurm -> /home/ladunga/sladunga/chipathlon/bowtie2indexmouse.slurm
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-rw-r----- 1 sladunga ladunga 888467894 Apr 18 12:57 GRCm38.1.bt2
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-rw-r----- 1 sladunga ladunga 663195880 Apr 18 12:57 GRCm38.2.bt2
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-rw-r----- 1 sladunga ladunga 6119 Apr 18 11:23 GRCm38.3.bt2
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-rw-r----- 1 sladunga ladunga 663195875 Apr 18 11:23 GRCm38.4.bt2
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-rw-r----- 1 sladunga ladunga 23 Apr 18 11:22 GRCm38.err
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-rw-r----- 1 sladunga ladunga 11771 Apr 18 14:24 GRCm38.out
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-rw-r----- 1 sladunga ladunga 888467894 Apr 18 14:24 GRCm38.rev.1.bt2
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-rw-r----- 1 sladunga ladunga 663195880 Apr 18 14:24 GRCm38.rev.2.bt2
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-rw-r----- 1 sladunga ladunga 69219 Apr 18 11:56 mm10-blacklist.bed
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-rw-r----- 1 sladunga ladunga 72057 Jan 25 2013 mm9-blacklist.bed
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-rw-r----- 1 sladunga ladunga 62943 Apr 18 11:28 mm9-blacklist_nochr.bed
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-rwxrwxr-x 1 sladunga ladunga 898035336 Mar 8 18:45 Mus_musculus.GRCm38.84.gtf
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-rw-r--r-- 1 sladunga ladunga 2776390504 Feb 25 02:30 Mus_musculus.GRCm38.dna.primary_assembly.fa |
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\ No newline at end of file |