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=== Alignment=== ====Pair End Mode==== {|style="font-size:80%;" |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)''' |- | SRR1232302_1_val_1.fq.gz_bismark_bt2_PE_report.txt||10896020||266017||2.40%||10986559||540111||45475||311108||558390||2521979||7009496||49.20%||1.80%||4.20% |- | SRR1232303_1_val_1.fq.gz_bismark_bt2_PE_report.txt||20216162||532701||2.60%||21017209||877814||62873||428697||973603||4695560||13978662||47.40%||1.30%||3.00% |- | SRR1232304_1_val_1.fq.gz_bismark_bt2_PE_report.txt||9233853||52146||0.60%||2154088||104373||8962||61461||113360||495917||1370015||47.90%||1.80%||4.30% |- | SRR1232305_1_val_1.fq.gz_bismark_bt2_PE_report.txt||19402159||359121||1.90%||14853592||750976||48615||303789||702872||3436588||9610752||51.70%||1.40%||3.10% |- | SRR1232306_1_val_1.fq.gz_bismark_bt2_PE_report.txt||51400600||1780106||3.50%||71928234||3884870||188607||772020||3360341||16663027||47059369||53.60%||1.10%||1.60% |- | SRR1232307_1_val_1.fq.gz_bismark_bt2_PE_report.txt||15015151||255663||1.70%||10806322||480441||44420||298374||509555||2351403||7122129||48.50%||1.90%||4.00% |- | SRR1232308_1_val_1.fq.gz_bismark_bt2_PE_report.txt||32508902||278849||0.90%||11147653||519877||35048||231897||507661||2493803||7359367||50.60%||1.40%||3.10% |- | SRR1232309_1_val_1.fq.gz_bismark_bt2_PE_report.txt||28578330||270922||0.90%||10742909||496990||27651||125158||386967||2329220||7376923||56.20%||1.20%||1.70% |- | SRR1232310_1_val_1.fq.gz_bismark_bt2_PE_report.txt||23879809||240025||1.00%||9580472||431160||36022||285577||493439||2136766||6197508||46.60%||1.70%||4.40% |- | SRR1232311_1_val_1.fq.gz_bismark_bt2_PE_report.txt||6078443||57482||0.90%||2159612||91805||6617||49301||91535||469450||1450904||50.10%||1.40%||3.30% |- | SRR1232312_1_val_1.fq.gz_bismark_bt2_PE_report.txt||9216625||194894||2.10%||8091546||392407||33197||226776||428295||1871966||5138905||47.80%||1.70%||4.20% |- |} ====Bsmap Alignment==== * Bsmap can use 16 CPU, however, with only 8G memory. it is different with bismark. in bismark memory usage is proportional with CUP number with 3G. #!/bin/csh #PBS -n Xie.LUN.SRR1232302_1.fastq.gz #PBS -q glean #PBS -l nodes=1:ppn=16 #PBS -l walltime=72:00:00 #PBS -o SRR1232302_1.fastq.gz.trim.log #PBS -e SRR1232302_1.fastq.gz.trim.err #PBS -V #PBS -M shihcheng.guo@gmail.com #PBS -m abe #PBS -A k4zhang-group cd /oasis/tscc/scratch/shg047/Xliu2014/fastq bsmap -u -s 12 -v 0.04 -p 16 -a ../fastq2_trim/SRR1232302_1_val_1.fq.gz -b ../fastq2_trim/SRR1232302_2_val_2.fq.gz -d /home/shg047/db/hg19/meth/bismark/hg19.fa -o ../bsmap/SRR1232302_1.bam * two job failed since glean. and this time pdafm were used to re-alignment. Resubmit (Feb/18/2016) cd /home/shg047/oasis/Xliu2014/fastq qsub SRR1232310_1.fastq.gz.job qsub SRR1232312_1.fastq.gz.job * two job completed (Feb/16/2016) and all the alignment were succeeded.the updated mapping statisitic {|style="font-size:80%;" |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)''' |- | SRR1232302_1_val_1.fq.gz_bismark_bt2_PE_report.txt||10879469||8166399||75.10%||283705221||14059544||396832||1083414||14827795||65987979||187349657||48.70%||0.60%||0.60% |- | SRR1232303_1_val_1.fq.gz_bismark_bt2_PE_report.txt||20185783||15643793||77.50%||538753835||24467542||731361||1999839||29198598||125132925||357223570||45.60%||0.60%||0.60% |- | SRR1232304_1_val_1.fq.gz_bismark_bt2_PE_report.txt||11064669||8668123||78.30%||301062107||14716791||435437||1166303||16357108||70648275||197738193||47.40%||0.60%||0.60% |- | SRR1232305_1_val_1.fq.gz_bismark_bt2_PE_report.txt||19379802||11358953||58.60%||405848758||21963190||606473||1550397||22103090||96959575||262666033||49.80%||0.60%||0.60% |- | SRR1232306_1_val_1.fq.gz_bismark_bt2_PE_report.txt||51331076||39232137||76.40%||1375770206||70954836||1959550||5129368||73767418||324505783||899453251||49.00%||0.60%||0.60% |- | SRR1232307_1_val_1.fq.gz_bismark_bt2_PE_report.txt||14987691||8977542||59.90%||312378988||14249586||467917||1334605||15164065||70650657||210512158||48.40%||0.70%||0.60% |- | SRR1232308_1_val_1.fq.gz_bismark_bt2_PE_report.txt||35378719||20706958||58.50%||723041259||35238860||1069487||2948419||35619931||165087550||483077012||49.70%||0.60%||0.60% |- | SRR1232309_1_val_1.fq.gz_bismark_bt2_PE_report.txt||34228833||20426178||59.70%||704014483||32162156||1007755||2905755||30199793||156286525||481452499||51.60%||0.60%||0.60% |- | SRR1232310_1_val_1.fq.gz_bismark_bt2_PE_report.txt||23850149||17995294||75.50%||563331726||27402528||831180||2213192||31796570||132428948||368659308||46.30%||0.60%||0.60% |- | SRR1232311_1_val_1.fq.gz_bismark_bt2_PE_report.txt||12142320||8808806||72.50%||272573717||13022456||405024||1118769||14270047||63239639||180517782||47.70%||0.60%||0.60% |- | SRR1232312_1_val_1.fq.gz_bismark_bt2_PE_report.txt||6133332||4094748||66.80%||142984922||6981841||202170||531307||8206242||33563875||93499487||46.00%||0.60%||0.60% |- | SRR1232313_1_val_1.fq.gz_bismark_bt2_PE_report.txt||32727127||23917117||73.10%||833607030||42703068||1162364||3069766||42946919||194253467||549471446||49.90%||0.60%||0.60% |- |}
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