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Disk usage

Disk usage. -rw-rw-r-- 1 mozhiyan samplers 1019619 Aug 22 18:32 23.seq -rw-rw-r-- 1 mozhiyan samplers 592 Aug 22 19:18 23.seq.blast1 -rw-rw-r-- 1 mozhiyan samplers 1000001 Aug 22 19:19 23.seq.conseq -rw-rw-r-- 1 mozhiyan samplers 9719 Aug 22 19:30 23.seq.gff

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Disk usage

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  1. Disk usage -rw-rw-r-- 1 mozhiyan samplers 1019619 Aug 22 18:32 23.seq -rw-rw-r-- 1 mozhiyan samplers 592 Aug 22 19:18 23.seq.blast1 -rw-rw-r-- 1 mozhiyan samplers 1000001 Aug 22 19:19 23.seq.conseq -rw-rw-r-- 1 mozhiyan samplers 9719 Aug 22 19:30 23.seq.gff -rw-rw-r-- 1 mozhiyan samplers 1019619 Aug 22 19:09 23.seq.masked -rw-rw-r-- 1 mozhiyan samplers 7112 Aug 22 19:30 23.seq.twinscan -rw-r--r-- 1 pflicek samplers 7920 Oct 2 23:40 23.seq.twinscan13.N1 -rw-r--r-- 1 pflicek samplers 7921 Oct 6 00:19 23.seq.twinscan13.N10 -rw-r--r-- 1 pflicek samplers 7058 Oct 6 09:05 23.seq.twinscan13.N30 -rw-rw-r-- 1 mozhiyan samplers 1109 Aug 22 19:30 23.seq.twinscan.progress -rw-rw-r-- 1 mozhiyan samplers 65 Aug 22 19:30 23.seq.twinscan.times -rw-r--r-- 1 pflicek samplers 15927 Oct 6 12:26 23.twinscan13.N10.gff -rw-r--r-- 1 pflicek samplers 15570 Oct 6 12:21 23.twinscan13.N1.gff -rw-r--r-- 1 pflicek samplers 14094 Oct 6 12:32 23.twinscan13.N30.gff -rw-r--r-- 1 mozhiyan samplers 0 Aug 22 19:09 human_v_mouse-c1-f23.e317629 -rw-r--r-- 1 mozhiyan samplers 142 Aug 22 19:19 human_v_mouse-c1-f23.e320711 -rw-r--r-- 1 mozhiyan samplers 479 Aug 22 19:09 human_v_mouse-c1-f23.o317629 -rw-r--r-- 1 mozhiyan samplers 544 Aug 22 19:30 human_v_mouse-c1-f23.o320711 -rw-rw-r-- 1 mozhiyan samplers 195 Aug 22 19:00 pbs.script -rw-rw-r-- 1 mozhiyan samplers 195 Aug 22 19:19 sge.script 3.1Mb

  2. New masking Use UCSC RepeatMasker table for masking -rw-r--r-- 1 jeltje samplers 70178 Jan 29 17:06 23.repeats lrwxrwxrwx 1 jeltje samplers 52 Jan 29 17:00 23.seq -> /bio/pro/human/NCBI34/chr_split/1/fragment_23/23.seq -rw-r--r-- 1 jeltje samplers 1000012 Jan 29 17:18 23.seq.masked Then mask pseudogenes -rw-r--r-- 1 jeltje samplers 1000012 Feb 2 10:10 23.seq.pmasked.masked -rw-r--r-- 1 jeltje samplers 88 Feb 2 10:10 23.masked.txt 23.repeats and 23.masked.txt are gtf files that can be used to mask the genome sequence Remove 23.seq? Create ONE masked seq? (but am still editing pseudogene masking) Remove all sequences in old runs and keep 'mask' gtf tables and chrN.fa sequences in chr_seq?

  3. Pseudogene prediction -rw-r--r-- 1 jeltje samplers 10943 Jan 30 10:00 23.1.gff -rw-r--r-- 1 jeltje samplers 449 Feb 2 10:06 23.1.introns -rw-r--r-- 1 jeltje samplers 42 Feb 2 10:10 23.1.pseudo -rw-r--r-- 1 jeltje samplers 244 Feb 2 10:06 23.1.RS_hits -rw-r--r-- 1 jeltje samplers 442 Feb 2 10:32 23.genes.introns -rw-r--r-- 1 jeltje samplers 217 Feb 2 10:32 23.genes.RS_hits -rw-r--r-- 1 jeltje samplers 88 Feb 2 10:10 23.masked.txt -rw-r--r-- 1 jeltje samplers 70178 Jan 29 17:06 23.repeats lrwxrwxrwx 1 jeltje samplers 52 Jan 29 17:00 23.seq -> /bio/pro/human/NCBI34/chr_split/1/fragment_23/23.seq -rw-r--r-- 1 jeltje samplers 10664 Feb 2 10:32 23.seq.gff -rw-r--r-- 1 jeltje samplers 1000012 Jan 29 17:18 23.seq.masked -rw-r--r-- 1 jeltje samplers 751913 Jan 30 09:47 23.seq.masked.blast1 -rw-r--r-- 1 jeltje samplers 1050411 Jan 30 09:49 23.seq.masked.blast2 -rw-r--r-- 1 jeltje samplers 1000060 Jan 30 09:49 23.seq.masked.conseq lrwxrwxrwx 1 jeltje samplers 13 Jan 30 09:36 23.seq.masked.masked -> 23.seq.masked -rw-r--r-- 1 jeltje samplers 1096 Jan 30 09:47 23.seq.masked.stage2db.xnd -rw-r--r-- 1 jeltje samplers 2550349 Jan 30 09:47 23.seq.masked.stage2db.xns -rw-r--r-- 1 jeltje samplers 1304 Jan 30 09:47 23.seq.masked.stage2db.xnt -rw-r--r-- 1 jeltje samplers 8309 Jan 30 09:59 23.seq.masked.twinscan -rw-r--r-- 1 jeltje samplers 2974 Jan 30 10:00 23.seq.masked.twinscan.progress -rw-r--r-- 1 jeltje samplers 63 Jan 30 10:00 23.seq.masked.twinscan.times -rw-r--r-- 1 jeltje samplers 1000012 Feb 2 10:10 23.seq.pmasked.masked -rw-r--r-- 1 jeltje samplers 1836 Feb 2 10:35 pgene.reason

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