Ns126:Encode Methylation: Difference between revisions
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#PBS -l walltime=72:00:00 | #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 | 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 | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''N(reads)''' | |||
| align="center" style="background:#f0f0f0;"|'''N(mapped)''' | |||
| align="center" style="background:#f0f0f0;"|'''P(mapping)''' | |||
| align="center" style="background:#f0f0f0;"|'''N(C)''' | |||
| align="center" style="background:#f0f0f0;"|'''N(MCPG)''' | |||
| align="center" style="background:#f0f0f0;"|'''N(MCHG)''' | |||
| align="center" style="background:#f0f0f0;"|'''N(MCHH)''' | |||
| align="center" style="background:#f0f0f0;"|'''N(UCPG)''' | |||
| align="center" style="background:#f0f0f0;"|'''N(UCHG)''' | |||
| align="center" style="background:#f0f0f0;"|'''N(UCHH)''' | |||
| align="center" style="background:#f0f0f0;"|'''P(MCPG)''' | |||
| align="center" style="background:#f0f0f0;"|'''P(MCHG)''' | |||
| align="center" style="background:#f0f0f0;"|'''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% | |||
|- | |||
| | |||
|} | |||
{| {{table}} | {| {{table}} |
Revision as of 19:57, 14 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
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% |
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% |