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===Analysis of low-pass sequencing data.=== *The first round of low-pass sequencing was done in HL101 run (SE60bp+index), lane 7-8. *I ran tophat on each data set, using mouse gene annotation as the model. less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx3.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx3.txt.gz > RNAseq_Indx3.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx4.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx4.txt.gz > RNAseq_Indx4.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx5.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx5.txt.gz > RNAseq_Indx5.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx6.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx6.txt.gz > RNAseq_Indx6.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx7.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx7.txt.gz > RNAseq_Indx7.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx8.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx8.txt.gz > RNAseq_Indx8.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx9.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx9.txt.gz > RNAseq_Indx9.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx10.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx10.txt.gz > RNAseq_Indx10.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx11.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx11.txt.gz > RNAseq_Indx11.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx12.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx12.txt.gz > RNAseq_Indx12.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx13.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx13.txt.gz > RNAseq_Indx13.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx14.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx14.txt.gz > RNAseq_Indx14.fq less /home/kunzhang/SeqStore/110902_HL101/s_7_Indx15.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_8_Indx15.txt.gz > RNAseq_Indx15.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx3 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx3.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx4 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx4.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx5 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx5.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx6 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx6.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx7 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx7.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx8 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx8.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx9 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx9.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx10 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx10.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx11 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx11.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx12 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx12.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx13 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx13.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx14 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx14.fq /home/kunzhang/softwares/tophat-latest/tophat -p 8 --solexa1.3-quals -o tophat_Mm_Indx15 -G /GenomeDB/UCSC/Mus_musculus/mm9/Annotation/Genes/genes.gtf /GenomeDB/UCSC/Mus_musculus/mm9/Sequence/BowtieIndex/genome RNAseq_Indx15.fq *Then I checked the tophat_Mm_IndxN/logs/bowtie.left_kept_reads.fixmap.log files, and used the mapping rates in these files as the proxy of the true mapping rates. {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample Name''' | align="center" style="background:#f0f0f0;"|'''Index''' | align="center" style="background:#f0f0f0;"|'''Qualty-filtered reads''' | align="center" style="background:#f0f0f0;"|'''Uniquely mappable reads''' | align="center" style="background:#f0f0f0;"|'''Non-mappable reads''' | align="center" style="background:#f0f0f0;"|'''Mapping rate''' |- | E9.5||Indx3||3,775,311||2,715,872||1,014,808||71.9% |- | E11.5||Indx4||3,987,505||2,710,512||1,238,018||68.0% |- | wt E13.5m1||Indx5||4,212,162||2,921,411||1,250,730||69.4% |- | wt E13.5f1||Indx6||3,557,137||2,506,010||1,019,618||70.5% |- | E9.5||Indx7||5,628,397||3,964,069||1,571,087||70.4% |- | E11.5||Indx8||6,095,896||4,322,793||1,687,193||70.9% |- | wt E13.5m1||Indx9||6,284,443||4,290,999||1,925,123||68.3% |- | wt E13.5m2||Indx10||4,649,460||3,276,710||1,316,390||70.5% |- | wt E13.5f1||Indx11||5,953,433||4,199,249||1,693,646||70.5% |- | wt E13.5f2||Indx12||6,712,315||4,671,588||1,969,301||69.6% |- | KO E13.5m||Indx13||4,954,624||3,517,633||1,380,709||71.0% |- | KO E13.5f1||Indx14||7,223,059||5,137,419||1,999,302||71.1% |- | KO E13.5f2||Indx15||8,053,410||5,681,254||2,272,034||70.5% |- | |} *Conclusions: **The mapping rate is consistently at ~70% across all libraries. **To generate roughly 20 millions mappable reads in each library, we need 4-5 HiSeq sequencing lanes.
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