Ns126:Encode Methylation: Difference between revisions
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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 | 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 | ||
**With above setting, the alignment time usage is about 16 hours. | |||
**The time is propotional to the size of the fastq file. | |||
Revision as of 01:17, 15 January 2016
RRBS Data Analysis to Encode Project
Aim
- Aim 1: methylation block with RRBS dataset
Background
- 1, Encode: http://genome.ucsc.edu/ENCODE/downloads.html
- 2, Encode|RRBS1: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/
- 3, Encode|RRBS2: http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=437674359_aUhx08DjchWwtBjyCYv61EB7Yy8S&c=chr1&g=wgEncodeHaibMethylRrbs
- big problem for the fastq files from the above link. 1) not fastq but rather RAS file 2) reads is not true reads.
- 4, Encode|Methy450K: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/
- 5, Encode|software: https://www.encodeproject.org/software/
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, so I extend the walltime to 72 hours.
#PBS -q glean #PBS -l nodes=1:ppn=8 #PBS -l walltime=72:00:00 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
- With above setting, the alignment time usage is about 16 hours.
- The time is propotional to the size of the fastq file.
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% |