Ns126:Encode Methylation

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Revision as of 19:53, 14 January 2016 by >Shicheng (→‎Alignment)
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RRBS Data Analysis to Encode Project

Aim

  • Aim 1: methylation block with RRBS dataset


Background

Method

Data Download

Fastq and bed files can be downloaded from Encode Project. 101 RRBS data (bed files) were downloaded. 2,646,999 CpG loci were covered by 101 RRBS data while 866,979 CpG loci (32.8%) were detected in at least 80% samples.

Result

Alignment

  • maybe walltime time is too short, not all the samples were aligned completely.
* bismark --bowtie2 --phred64-quals --fastq -L 30 -N 1 --multicore 2 /home/shg047/db/hg19/meth/bismark ../fastq_trim/HOT197_trimmed.fq.gz -o ../bam2
Sample N(reads) N(mapped) P(mapping) N(C) N(MCPG) N(MCHG) N(MCHH) N(UCPG) N(UCHG) N(UCHH) P(MCPG) P(MCHG) P(MCHH)
ENCFF000LUP 12830405 2122731 16.50% 23121452 1755272 39237 63026 4964667 5412746 10886504 26.10% 0.70% 0.60%
ENCFF000LUQ 5561765 2658766 47.80% 29121454 1939714 57696 100525 7299273 6782758 12941488 21.00% 0.80% 0.80%
ENCFF000LVA 8018858 1683010 21.00% 15937339 1377038 59505 190243 2691809 3785119 7833625 33.80% 1.50% 2.40%
ENCFF000LVB 11054693 2404800 21.80% 22228173 1455733 40643 119125 3161543 4987120 12464009 31.50% 0.80% 0.90%
ENCFF000LVE 10736789 3048286 28.40% 32772970 1631989 49822 88996 8206874 7496120 15299169 16.60% 0.70% 0.60%
ENCFF000LVK 8542224 2399071 28.10% 27152898 1893547 51170 70824 6965949 6095807 12075601 21.40% 0.80% 0.60%
ENCFF000LVN 13332915 4317747 32.40% 31477310 1393770 79434 352105 2252186 6961310 20438505 38.20% 1.10% 1.70%
ENCFF000LVO 16368796 2638210 16.10% 20542040 994068 43080 182778 2631559 4373546 12317009 27.40% 1.00% 1.50%
ENCFF000LVR 16091088 2615346 16.30% 22490847 1312651 47566 188989 3319980 4807814 12813847 28.30% 1.00% 1.50%
ENCFF000LVU 13225098 1999398 15.10% 18717042 1158340 37399 98519 2836054 4402056 10184674 29.00% 0.80% 1.00%
ENCFF000LVV 11857985 3571402 30.10% 38309965 2844978 73249 122725 8543749 9108762 17616502 25.00% 0.80% 0.70%
ENCFF000LWE 21908830 2413683 11.00% 24666773 1746092 71933 124011 4886835 5721680 12116222 26.30% 1.20% 1.00%
ENCFF000LWL 16598050 3530912 21.30% 32715178 1675159 59309 192601 5947741 7094553 17745815 22.00% 0.80% 1.10%
ENCFF000LWP 16429464 2721119 16.60% 28744997 1773533 43976 80430 6212197 6572632 14062229 22.20% 0.70% 0.60%
ENCFF000LWS 6325597 1224397 19.40% 13284708 1257780 29276 46149 2987604 3195673 5768226 29.60% 0.90% 0.80%
ENCFF000LWW 16821394 2133899 12.70% 22603245 1722157 39949 68530 4343561 5191728 11237320 28.40% 0.80% 0.60%
ENCFF000LWX 21208447 13218301 62.30% 145215571 9668358 223882 356827 34200783 33840207 66925514 22.00% 0.70% 0.50%
ENCFF000LXB 18551059 3078942 16.60% 33082876 1775486 66300 106053 8382345 7598213 15154479 17.50% 0.90% 0.70%