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===Alignment of Agi26k oligo reads to full reference=== *~33% alignment rate for 0gap expected because ~2/3 Indx10 of the reads are Dan's probes *~33% alignment rate for 20gap expected because ~2/3 Indx12 of the reads are Dan's probes *Using the same reasoning as for the CA12k Oligo alignment, redid alignment without "-k 1" Fasta reference file (50bp long): Agi26k_corrected.fa 0 gap aligned with custom parameters: /home/kunzhang/softwares/bowtie2-latest/bowtie2 --phred64 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26k_corrected -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx10.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2all_revcomp_0gap.txt & 16368416 reads; of these: 16368416 (100.00%) were unpaired; of these: 10066426 (61.50%) aligned 0 times 1491167 (9.11%) aligned exactly 1 time 4810823 (29.39%) aligned >1 times 38.50% overall alignment rate [[File:Agi26k_0gapAlignedtoAllCustomScorePenalties.JPG|700px]] *4,848,010 aligned to 0gap probes *1,453,980 aligned to 20gap probes 20 gap aligned with custom parameters: /home/kunzhang/softwares/bowtie2-latest/bowtie2 --phred64 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26k_corrected -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx12.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2all_revcomp_20gap.txt & 17308686 reads; of these: 17308686 (100.00%) were unpaired; of these: 12337494 (71.28%) aligned 0 times 1022448 (5.91%) aligned exactly 1 time 3948744 (22.81%) aligned >1 times 28.72% overall alignment rate [[File:Agi26k_20gapAlignedtoAllCustomScorePenalties.JPG|700px]] *1,033,711 aligned to 0gap probes *3,937,481 aligned to 20gap probes 0 gap aligned with default parameters: /home/kunzhang/softwares/bowtie2-latest/bowtie2 --phred64 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26k_corrected -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx10.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2all_revcomp_0gap_default.txt & 16368416 reads; of these: 16368416 (100.00%) were unpaired; of these: 11414712 (69.74%) aligned 0 times 4923826 (30.08%) aligned exactly 1 time 29878 (0.18%) aligned >1 times 30.26% overall alignment rate [[File:Agi26k_0gapAlignedtoAlldefault.JPG|700px]] *4,951,251 aligned to 0gap *2,453 aligned to 20gap probes 20 gap aligned with default parameters: /home/kunzhang/softwares/bowtie2-latest/bowtie2 --phred64 -x /home/mzcai/InSitu_HL155_130628_Analysis/Agi26k_corrected -q /home/mzcai/InSitu_HL155_130628_Analysis/s_3_1_Indx12.txt > /home/mzcai/InSitu_HL155_130628_Analysis/Readsalign2all_revcomp_20gap_default.txt & 17308686 reads; of these: 17308686 (100.00%) were unpaired; of these: 13257038 (76.59%) aligned 0 times 4027036 (23.27%) aligned exactly 1 time 24612 (0.14%) aligned >1 times 23.41% overall alignment rate [[File:Agi26k_20gapAlignedtoAlldefault.JPG|700px]] *2,627 aligned to 0gap *4,049,021 aligned to 20gap
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