Matt:LabNotes/2014-10-31
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RT Primer RNA-Seq Analysis
- Library Matt:LabNotes/2014-9-25
Align with Tophat2 to hg19
~/scratch/RTprimer_Analysis$ /home/kunzhang/softwares/tophat-2.0.6.Linux_x86_64/tophat2 -o tophat_hg19unmask_Indx26_RanHex --solexa1.3-quals ~/LTS/Genomes/hg19 s_8_1_Indx26.txt ~/scratch/RTprimer_Analysis$ /home/kunzhang/softwares/tophat-2.0.6.Linux_x86_64/tophat2 -o tophat_hg19unmask_Indx27_dT --solexa1.3-quals ~/LTS/Genomes/hg19 s_8_1_Indx27.txt ~/scratch/RTprimer_Analysis$ /home/kunzhang/softwares/tophat-2.0.6.Linux_x86_64/tophat2 -o tophat_hg19unmask_Indx28_FISSEQRT --solexa1.3-quals ~/LTS/Genomes/hg19 s_8_1_Indx28.txt ~/scratch/RTprimer_Analysis$ /home/kunzhang/softwares/tophat-2.0.6.Linux_x86_64/tophat2 -o tophat_hg19unmask_Indx29_Top48 --solexa1.3-quals ~/LTS/Genomes/hg19 s_8_1_Indx29.txt
- RanHex
586553 reads; of these: 586553 (100.00%) were unpaired; of these: 251516 (42.88%) aligned 0 times 196622 (33.52%) aligned exactly 1 time 138415 (23.60%) aligned >1 times 57.12% overall alignment rate
- dT
432896 reads; of these: 432896 (100.00%) were unpaired; of these: 103736 (23.96%) aligned 0 times 215595 (49.80%) aligned exactly 1 time 113565 (26.23%) aligned >1 times 76.04% overall alignment rate
- FISSEQRT
529281 reads; of these: 529281 (100.00%) were unpaired; of these: 199427 (37.68%) aligned 0 times 205336 (38.80%) aligned exactly 1 time 124518 (23.53%) aligned >1 times 62.32% overall alignment rate
- Top48
523107 reads; of these: 523107 (100.00%) were unpaired; of these: 165872 (31.71%) aligned 0 times 229706 (43.91%) aligned exactly 1 time 127529 (24.38%) aligned >1 times 68.29% overall alignment rate