Rui:Data Analysis: Difference between revisions
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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
- Haplotyping 6.21.11
- RNAseq analysis from 7.18.11
- RNAseq analysis on HL098
- Rui:RNAseq analysis on HL098lRNAseq analysis on HL098
- RNAseq analysis on HL099
RNAseq analysis on HL098
Database download
iGenome collection [4], save in ~/iGenome/
- wget ftp://igenome:G3nom3s4u@ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
- wget ftp://igenome:G3nom3s4u@ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz
- tar -zxvf Homo_sapiens_UCSC_hg19.tar.gz
- tar -zxvf Mus_musculus_UCSC_mm9.tar.gz
- 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...)