NGS_Illumina类# Biology - 生物学i*i2012-09-14 07:091 楼上个月一个dreamcompany,面完说2周给消息,现在3周了,followup也没回复。伤感下。move on, 大家都加油啊~
s*n2012-09-14 07:092 楼话说和一MM同租一二室一厅。MM自搬来后就时不时偷看我。我心头暗爽。终于在一个月黑风高的下午,我们XE的合体了。。。事后,我问她,是不是早就盼着这一天呢?她HLL的来句,嗯,这俩天就看你色迷迷的看着我。怕你把我先奸后杀,提前把你收了提前~~~~。。。。。收了~~~~。。。。。后来知道,她比我大4岁。。。。
g*y2012-09-14 07:093 楼欢迎讨论,特别是各种程序的调用参数 。。。http://dl.dropbox.com/u/62547840/NGS_Illumina.pmhttp://dl.dropbox.com/u/62547840/NGS_Illumina.plscreen output:Illumina 1.3+ fastq format: ASCII(min, max) = (66, 102)2012/08/25 11:41:15 START maq ill2sanger Run1_testicular-28T_lane2_read1_sequence.txt Testis_T28_read1_sanger.fq2012/08/25 11:42:57 SUCCESS after running 0 hours 1 minutes 42 seconds2012/08/25 11:42:57 START maq ill2sanger Run1_testicular-28T_lane2_read2_sequence.txt Testis_T28_read2_sanger.fq2012/08/25 11:44:37 SUCCESS after running 0 hours 1 minutes 40 seconds2012/08/25 11:44:37 START fastx_quality_stats -Q 33 -i Testis_T28_read1_sanger.fq -o ./qcstats/Testis_T28_read1_sanger.fq_stats.txt2012/08/25 11:49:13 SUCCESS after running 0 hours 4 minutes 36 seconds2012/08/25 11:49:13 START fastq_quality_boxplot_graph.sh -i ./qcstats/Testis_T28_read1_sanger.fq_stats.txt -o ./qcstats/Testis_T28_read1_sanger.fq_stats.png -t "Testis_T28_read1_sanger.fq"2012/08/25 11:49:13 SUCCESS after running 0 hours 0 minutes 0 seconds2012/08/25 11:49:13 START fastx_quality_stats -Q 33 -i Testis_T28_read2_sanger.fq -o ./qcstats/Testis_T28_read2_sanger.fq_stats.txt2012/08/25 11:53:51 SUCCESS after running 0 hours 4 minutes 38 seconds2012/08/25 11:53:51 START fastq_quality_boxplot_graph.sh -i ./qcstats/Testis_T28_read2_sanger.fq_stats.txt -o ./qcstats/Testis_T28_read2_sanger.fq_stats.png -t "Testis_T28_read2_sanger.fq"2012/08/25 11:53:51 SUCCESS after running 0 hours 0 minutes 0 seconds2012/08/25 11:53:51 START bwa aln -t 8 /data/public/reference_genomes/genome_hg18.fa Testis_T28_read1_sanger.fq > ./bam/Testis_T28.read1.sai2012/08/25 12:42:44 SUCCESS after running 0 hours 48 minutes 53 seconds2012/08/25 12:42:44 START bwa aln -t 8 /data/public/reference_genomes/genome_hg18.fa Testis_T28_read2_sanger.fq > ./bam/Testis_T28.read2.sai2012/08/25 13:33:10 SUCCESS after running 0 hours 50 minutes 26 seconds2012/08/25 13:33:10 START bwa sampe /data/public/reference_genomes/genome_hg18.fa ./bam/Testis_T28.read1.sai ./bam/Testis_T28.read2.sai Testis_T28_read1_sanger.fq Testis_T28_read2_sanger.fq > ./bam/Testis_T28.sam2012/08/25 13:50:34 SUCCESS after running 0 hours 17 minutes 24 seconds2012/08/25 13:50:34 START samtools import /data/public/reference_genomes/genome_hg18.fa.fai ./bam/Testis_T28.sam ./bam/Testis_T28.bam2012/08/25 14:03:10 SUCCESS after running 0 hours 12 minutes 36 seconds2012/08/25 14:03:10 START samtools sort ./bam/Testis_T28.bam ./bam/Testis_T28.sorted2012/08/25 14:25:58 SUCCESS after running 0 hours 22 minutes 48 seconds2012/08/25 14:25:58 START samtools index ./bam/Testis_T28.sorted.bam2012/08/25 14:26:42 SUCCESS after running 0 hours 0 minutes 44 seconds2012/08/25 14:26:42 START java -Xmx4g -jar /home/gmslz/tools/picard-tools-1.44/MarkDuplicates.jar VALIDATION_STRINGENCY=SILENT M=PCR_duplicates.M.txtREMOVE_DUPLICATES=true AS=true I=./bam/Testis_T28.sorted.bam O=./bam/Testis_T28.sorted.rmdup.bam2012/08/25 14:40:45 SUCCESS after running 0 hours 14 minutes 3 seconds2012/08/25 14:40:45 START java -Xmx4g -jar /home/gmslz/tools/picard-tools-1.44/AddOrReplaceReadGroups.jar RGID=lane1 RGLB=Testis_T28.fastq RGPL=IlluminaRGPU=run RGSM=Testis_T28 CREATE_INDEX=TRUE VALIDATION_STRINGENCY=SILENT I=./bam/Testis_T28.sorted.rmdup.bam O=./bam/Testis_T28.sorted.rmdup.rg.bam2012/08/25 14:52:13 SUCCESS after running 0 hours 11 minutes 28 seconds2012/08/25 14:52:13 START samtools index ./bam/Testis_T28.sorted.rmdup.rg.bam2012/08/25 14:52:59 SUCCESS after running 0 hours 0 minutes 46 seconds2012/08/25 14:53:00 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -TRealignerTargetCreator -l INFO -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod-R /data/public/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.sorted.rmdup.rg.bam -o ./snp_analysis_gatk/Testis_T28.intervals > ./log/Testis_T28.intervals.log2012/08/25 16:29:57 SUCCESS after running 1 hours 36 minutes 57 seconds2012/08/25 16:29:57 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T IndelRealigner -l INFO -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R /data/public/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.sorted.rmdup.rg.bam -targetIntervals ./snp_analysis_gatk/Testis_T28.intervals -o ./bam/Testis_T28.realigned.bam -stats ./bam/Testis_T28.realign.stats.txt > ./log/Testis_T28.realign.log2012/08/26 00:40:15 SUCCESS after running 8 hours 10 minutes 18 seconds2012/08/26 00:40:15 START samtools index ./bam/Testis_T28.realigned.bam2012/08/26 00:41:08 SUCCESS after running 0 hours 0 minutes 53 seconds2012/08/26 00:41:08 START java -Xmx4g -jar /home/gmslz/tools/picard-tools-1.44/SortSam.jar SO=coordinate VALIDATION_STRINGENCY=SILENT I=./bam/Testis_T28.realigned.bam O=./bam/Testis_T28.realigned.sorted.bam2012/08/26 00:52:36 SUCCESS after running 0 hours 11 minutes 28 seconds2012/08/26 00:52:36 START samtools index ./bam/Testis_T28.realigned.sorted.bam2012/08/26 00:53:21 SUCCESS after running 0 hours 0 minutes 45 seconds2012/08/26 00:53:21 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /home/gmslz/tools/picard-tools-1.44/FixMateInformation.jar SO=coordinateVALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=2000000 I=./bam/Testis_T28.realigned.sorted.bam O=./bam/Testis_T28.realigned.sorted.fixed.bam2012/08/26 01:14:28 SUCCESS after running 0 hours 21 minutes 7 seconds2012/08/26 01:14:28 START samtools index ./bam/Testis_T28.realigned.sorted.fixed.bam2012/08/26 01:15:13 SUCCESS after running 0 hours 0 minutes 45 seconds2012/08/26 01:15:13 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T CountCovariates-l INFO -nt 8 --downsample_to_coverage 10000 --default_platform Illumina -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -covDinucCovariate -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R /data/public/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.realigned.sorted.fixed.bam -recalFile ./snp_analysis_gatk/Testis_T28.recal.csv > ./log/Testis_T28.count.covariates.log2012/08/26 01:25:00 SUCCESS after running 0 hours 9 minutes 47 seconds2012/08/26 01:25:00 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -TTableRecalibration -l INFO --default_platform Illumina -R /data/public/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.realigned.sorted.fixed.bam -recalFile ./snp_analysis_gatk/Testis_T28.recal.csv --out ./bam/Testis_T28.final.recalibrated.bam > ./log/Testis_T28.recalibration.log2012/08/26 02:00:22 SUCCESS after running 0 hours 35 minutes 22 seconds2012/08/26 02:00:22 START samtools index ./bam/Testis_T28.final.recalibrated.bam2012/08/26 02:01:27 SUCCESS after running 0 hours 1 minutes 5 seconds2012/08/26 02:01:27 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T IndelGenotyperV2-l INFO --window_size 450 -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R/data/public/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.final.recalibrated.bam -o ./snp_analysis_gatk/Testis_T28.indels.vcf -bed ./snp_analysis_gatk/Testis_T28.indels.bed > ./log/Testis_T28.indels.log2012/08/26 02:40:46 SUCCESS after running 0 hours 39 minutes 19 seconds2012/08/26 02:40:46 START python /data/public/tools/gatk-v4333/Sting/python/makeIndelMask.py ./snp_analysis_gatk/Testis_T28.indels.bed 10 ./snp_analysis_gatk/Testis_T28.indels.mask.bed2012/08/26 02:40:46 SUCCESS after running 0 hours 0 minutes 0 seconds2012/08/26 02:40:46 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -T UnifiedGenotyper-l INFO -stand_call_conf 30 -stand_emit_conf 10 -pl SOLEXA -mmq 30 -mm40 3-D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R /data/public/reference_genomes/genome_hg18.fa -I ./bam/Testis_T28.final.recalibrated.bam -o ./snp_analysis_gatk/Testis_T28.raw.snps.vcf > ./log/Testis_T28.snp.log2012/08/26 04:48:58 SUCCESS after running 2 hours 8 minutes 12 seconds2012/08/26 04:48:58 START java -Xmx4g -Djava.io.tmpdir=/home/tmp/ -jar /data/public/tools/gatk-v4333/Sting/dist/GenomeAnalysisTK.jar -TVariantFiltration -l INFO --clusterSize 3 --clusterWindowSize 10 --filterExpression "DP <= 8" --filterName "DP8" --filterExpression "SB > -0.10" --filterName "StrandBias" --filterExpression "HRun > 8" --filterName "HRun8" --filterExpression "QD < 5.0" --filterName "QD5" --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" --filterName "hard2validate" -D /data/nextgen1/pipeline/dbsnp_130_hg18.rod -R /data/public/reference_genomes/genome_hg18.fa -B:variant,VCF ./snp_analysis_gatk/Testis_T28.raw.snps.vcf -B:mask,Bed ./snp_analysis_gatk/Testis_T28.indels.mask.bed --maskName InDel -o./snp_analysis_gatk/Testis_T28.snp.filtered.vcf > ./log/Testis_T28.snp.filter.log2012/08/26 04:53:29 SUCCESS after running 0 hours 4 minutes 31 seconds
z*t2012-09-14 07:098 楼求一并收【在 s***n 的大作中提到】: 话说和一MM同租一二室一厅。MM自搬来后就时不时偷看我。我心头暗爽。: 终于在一个月黑风高的下午,我们XE的合体了。。。: 事后,我问她,是不是早就盼着这一天呢?: 她HLL的来句,嗯,这俩天就看你色迷迷的看着我。怕你把我先奸后杀,提前把你收了: 提前~~~~。。。。。: 收了~~~~。。。。。: 后来知道,她比我大4岁。。。。
s*m2012-09-14 07:0911 楼xe? hll?【在 s***n 的大作中提到】: 话说和一MM同租一二室一厅。MM自搬来后就时不时偷看我。我心头暗爽。: 终于在一个月黑风高的下午,我们XE的合体了。。。: 事后,我问她,是不是早就盼着这一天呢?: 她HLL的来句,嗯,这俩天就看你色迷迷的看着我。怕你把我先奸后杀,提前把你收了: 提前~~~~。。。。。: 收了~~~~。。。。。: 后来知道,她比我大4岁。。。。
b*y2012-09-14 07:0912 楼I thought I knew how to use perl. Now I know that I am not even close.Thanks for sharing.
e*o2012-09-14 07:0915 楼many scientists using the old Perl as ten years ago.http://onyxneon.com/books/modern_perl/【在 b******y 的大作中提到】: I thought I knew how to use perl. Now I know that I am not even close.: Thanks for sharing.