Rui:Data Analysis: Difference between revisions

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>RuiLiu
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*[[Rui:Haplotyping 6.21.11|Haplotyping 6.21.11]]
*[[Rui:Haplotyping 6.21.11|Haplotyping 6.21.11]]
*[[Rui:RNAseq analysis from 7.18.11|RNAseq analysis from 7.18.11]]
*[[Rui:RNAseq analysis from 7.18.11|RNAseq analysis from 7.18.11]]
*[[Rui:RNAseq analysis on HL098|RNAseq analysis on HL098]]
*[[Rui:RNAseq analysis on HL098lRNAseq analysis on HL098]]
*[[Rui:RNAseq analysis on HL098lRNAseq analysis on HL098]]
*[[Rui:RNAseq analysis on HL099|RNAseq analysis on HL099]]
*[[Rui:RNAseq analysis on HL099|RNAseq analysis on HL099]]

Revision as of 23:18, 14 October 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]

Data analysis

RNAseq analysis on HL098

Database download

iGenome collection [4], save in ~/iGenome/

  • BowtieIndex: ~/iGenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex | ~/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex
  • Annotation: ~/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf

Tophat

nohup tophat -p 6 --solexa1.3-quals -o ./tophat-g/ -r 250 --mate-std-dev 80 -G ~/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/iGenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ./seq/s_1_1_Indx1.txt ./seq/s_1_2_Indx1.mod.txt

nohup tophat -p 6 --solexa1.3-quals -o ./tophat-g/ -r 250 --mate-std-dev 80 -G ~/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/iGenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ./seq/s_1_1_Indx2.txt ./seq/s_1_2_Indx2.mod.txt

Samtools and clonalreads removal

samtools flagstat accepted_hits.bam

~/RNAtools/removalclonalreads.pl accepted_hits.bam


Pair-end mapping ' ' ' ' ' Tophat ' ' ' ' ' removeClonalHits.pl ' ' ' ' ' ' '
file size fastq reads in reads out % options accepted hits reads hits pair/single Properly paired % of total mapped reads % of total pro-rm clonal reads % of total % of mappable reads then uniquely mapped % of total potential coverage
s_1_Indx1 s_1_1_Indx1 left read 2,307,029 2,300,738 0.9973 r:250 1,705,993 734,602 1,122,540 0.657998011 1,615,384 0.3501 1,191,029 0.2581 0.7373 1,160,079 0.2514 0.04640316
s_1_2_Indx1 right read 2,307,029 2,304,795 0.9990 STD:80 971,391 583,453 941,458 0.551853378
s_1_Indx1 s_1_1_Indx1 left read 2,307,029 2,300,738 0.9973 (+g) 1,733,904 746,989 1,156,628 0.667065766 1,643,007 0.3561 1,218,033 0.2640 0.7413 1,186,899 0.2572 0.04747596
s_1_2_Indx1 right read 2,307,029 2,304,795 0.9990 UCSC 986,915 577,276 965,638 0.556915492
s_1_Indx2 s_1_1_Indx2 left read 3,078,335 3,069,878 0.9973 r:250 3,882,019 1,679,990 2,750,090 0.70841745 3,678,987 0.5976 2,642,026 0.4291 0.7181 2,585,255 0.4199 0.1034102
s_1_2_Indx2 right read 3,078,335 3,075,318 0.9990 STD:80 2,202,029 1,131,929 2,293,768 0.590869854
s_1_Indx2 s_1_1_Indx2 left read 3,078,335 3,069,878 0.9973 (+g) 3,913,815 1,694,018 2,792,224 0.713427691 3,711,732 0.6029 2,674,065 0.4343 0.7204 2,617,136 0.4251 0.10468544
s_1_2_Indx2 right read 3,078,335 3,075,318 0.9990 UCSC 2,219,797 1,121,591 2,344,834 0.59911723

Cufflinks and cuffdiff

samtools view -h ../accepted_hits.bam > accepted_hits.sam (have to convert to sam first, i can't feed cufflinks with bam file --- error: segment fault...)

cufflinks -g ~/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf -m 250 -s 80 accepted_hits.sam (-g option is probably unnecessary...)