Matt:LabNotes/2014-10-31

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Revision as of 19:54, 31 October 2014 by >Mzcai (Created page with "==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...")
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RT Primer RNA-Seq Analysis

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