Rui:Data Analysis: Difference between revisions
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ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.unique.bam | wc -l | ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.unique.bam | wc -l | ||
49694 | 49694 | ||
===Reads=== | |||
Sorted Uniquely sorted % | |||
Indx1 163556 15899 | |||
Indx2 196625 16718 | |||
Indx3 127140 10123 | |||
Indx4 189464 13511 | |||
Indx5 9536 4856 | |||
Indx6 220670 12779 | |||
Indx7 185404 12479 | |||
Indx8 209445 14185 | |||
Indx9 175999 12100 | |||
Indx10 212683 13919 | |||
Indx11 188707 14591 | |||
Indx12 326082 16300 |
Revision as of 22:43, 22 June 2011
Examples
Jeff's samples: Kun:LabNotes/Haplotyping/2010-9-17
Transcriptome: Kun:LabNotes/SingleCellExpr/2011-6-13
Haplotyping: Kun:LabNotes/Haplotyping/2011-6-14
Haplotyping 6.21.11
Data
ruiliu@genome-miner:~$ cd /home/kunzhang/haplotyping/Data/HL095/
ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ ls -l s_4_Indx1.*
-rw-r--r-- 1 kunzhang kunzhang 114237942 2011-06-13 22:07 s_4_Indx1.bowtie.pileup -rw-r--r-- 1 kunzhang kunzhang 39977658 2011-06-13 21:28 s_4_Indx1.bowtie.sorted.bam -rw-r--r-- 1 kunzhang kunzhang 4442210 2011-06-13 22:05 s_4_Indx1.bowtie.sorted.unique.bam -rw-r--r-- 1 kunzhang kunzhang 278 2011-06-13 21:29 s_4_Indx1.bowtie.variants.txt -rw-r--r-- 1 kunzhang kunzhang 7103 2011-06-14 15:58 s_4_Indx1.hapCompare.txt -rw-r--r-- 1 kunzhang kunzhang 9399 2011-06-14 16:56 s_4_Indx1.idioGraph.txt -rw-r--r-- 1 kunzhang kunzhang 675115 2011-06-13 21:29 s_4_Indx1.log -rw-r--r-- 1 kunzhang kunzhang 273522562 2011-06-13 18:08 s_4_Indx1.txt
ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ less s_4_Indx1.bowtie.pileup
1 557399 C A 25 25 25 1 ^:A f 1 557400 A A 25 0 25 1 . f 1 557401 T T 25 0 25 1 . f 1 557402 C C 25 0 25 1 . f 1 557403 A A 25 0 25 1 . c 1 557404 C C 25 0 25 1 . g 1 557405 T T 25 0 25 1 . g 1 557406 A A 25 0 25 1 . g 1 557407 G G 25 0 25 1 . g 1 557408 A A 25 0 25 1 . e 1 557409 C C 25 0 25 1 . f
ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ more s_4_Indx11.log
/home/kunzhang/softwares/bowtie-latest/bowtie -k 1 -l 32 -n 2 -m 1 --best --quiet -p 4 /home/kunzhang/HsGenome/1KG.ref/HsB36m s_4_Indx 11.txt s_4_Indx11.bowtie.map.1 /home/kunzhang/Exome/Data/scripts/trimTerminalMismatches.pl < s_4_Indx11.bowtie.map.1 > s_4_Indx11.bowtie.map.2 /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/bowtie2sam.pl s_4_Indx11.bowtie.map.2 > s_4_Indx11.bowtie.sam /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools import /home/kunzhang/HsGenome/1KG.ref/human_b36_male.fa.gz.fai s_4_Indx 11.bowtie.sam s_4_Indx11.bowtie.bam [sam_header_read2] 114 sequences loaded. /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools sort s_4_Indx11.bowtie.bam s_4_Indx11.bowtie.sorted java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.38/MarkDuplicates.jar ASSUME_SORTED=TRUE REMOVE_DUPLICATES=TRUE INPUT=s_4_In dx11.bowtie.sorted.bam OUTPUT=s_4_Indx11.bowtie.sorted.unique.bam METRICS_FILE=dup.metric [Tue Jun 14 15:23:03 PDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=s_4_Indx11.bowtie.sorted.bam OUTPUT=s_4_Indx11.bowtie.sorted.uni que.bam METRICS_FILE=dup.metric REMOVE_DUPLICATES=true ASSUME_SORTED=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDL ES_FOR_READ_ENDS_MAP=8000 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 TMP_DIR =/tmp/kunzhang VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=fals e CREATE_MD5_FILE=false INFO 2011-06-14 15:23:03 MarkDuplicates Start of doWork freeMemory: 374846832; totalMemory: 377225216; maxMemory: 1908932608 INFO 2011-06-14 15:23:03 MarkDuplicates Reading input file and constructing read end information. INFO 2011-06-14 15:23:03 MarkDuplicates Will retain up to 7575129 data points before spilling to disk. INFO 2011-06-14 15:23:03 MarkDuplicates Assuming input is coordinate sorted. INFO 2011-06-14 15:23:06 MarkDuplicates Read 887559 records. 0 pairs never matched. INFO 2011-06-14 15:23:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 733397640; totalMemory: 925368320; maxMemory : 1908932608 INFO 2011-06-14 15:23:07 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2011-06-14 15:23:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2011-06-14 15:23:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2011-06-14 15:23:09 MarkDuplicates Sorting list of duplicate records. INFO 2011-06-14 15:23:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 923987040; totalMemory: 1410072576; maxMemo ry: 1908932608 INFO 2011-06-14 15:23:09 MarkDuplicates Marking 837865 records as duplicates. INFO 2011-06-14 15:23:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2011-06-14 15:23:12 MarkDuplicates Before output close freeMemory: 920285040; totalMemory: 1408237568; maxMemory: 1908932 608 INFO 2011-06-14 15:23:12 MarkDuplicates After output close freeMemory: 876964080; totalMemory: 1364918272; maxMemory: 19089326 08 [Tue Jun 14 15:23:12 PDT 2011] net.sf.picard.sam.MarkDuplicates done. Runtime.totalMemory()=1364918272 /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/human_b36_male.fa s_4_Indx1 1.bowtie.sorted.unique.bam > s_4_Indx11.bowtie.pileup Use of uninitialized value in print at /home/kunzhang/Exome/Data/scripts/pileup2variants.pl line 145. Use of uninitialized value in print at /home/kunzhang/Exome/Data/scripts/pileup2variants.pl line 145.
ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.bam | wc -l
887559
ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.unique.bam | wc -l
49694
Reads
Sorted Uniquely sorted % Indx1 163556 15899 Indx2 196625 16718 Indx3 127140 10123 Indx4 189464 13511 Indx5 9536 4856 Indx6 220670 12779 Indx7 185404 12479 Indx8 209445 14185 Indx9 175999 12100 Indx10 212683 13919 Indx11 188707 14591 Indx12 326082 16300