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

[1]

Transcriptome:
Kun:LabNotes/SingleCellExpr/2011-6-13

[2]

Haplotyping:
Kun:LabNotes/Haplotyping/2011-6-14

[3]

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