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====Align with Bowtie2 to total rRNA==== *Combine rRNA sequences and Mt_rRNA fasta sequences (from biomart, same ones used to design Top48 RT primers for mRNA enrich) **Build bowtie2 index mzcai@genome-miner:~/scratch/RanHex_EnrichmRNA$cat mart_export_exons_Mt_rRNA.fa mart_export_exons_rRNA.fa > mart_export_exons_totalrRNA.fa mzcai@genome-miner:~/scratch/RanHex_EnrichmRNA$bowtie2-build mart_export_exons_totalrRNA.fa tot_rRNA *Bowtie2 alignment mzcai@genome-miner:~/scratch/RanHex_EnrichmRNA/inVitroRTSeq$ bowtie2 --phred64 -x ~/scratch/RanHex_EnrichmRNA/tot_rRNA -q s_1_1_Indx26.txt > RanHex_bowtie2_totRNA.sam 5441 reads; of these: 5441 (100.00%) were unpaired; of these: 2964 (54.48%) aligned 0 times 2477 (45.52%) aligned exactly 1 time 0 (0.00%) aligned >1 times 45.52% overall alignment rate mzcai@genome-miner:~/scratch/RanHex_EnrichmRNA/inVitroRTSeq$ bowtie2 --phred64 -x ~/scratch/RanHex_EnrichmRNA/tot_rRNA -q s_1_1_Indx27.txt > dT_bowtie2_totRNA.sam 10905 reads; of these: 10905 (100.00%) were unpaired; of these: 9121 (83.64%) aligned 0 times 1783 (16.35%) aligned exactly 1 time 1 (0.01%) aligned >1 times 16.36% overall alignment rate mzcai@genome-miner:~/scratch/RanHex_EnrichmRNA/inVitroRTSeq$ bowtie2 --phred64 -x ~/scratch/RanHex_EnrichmRNA/tot_rRNA -q s_1_1_Indx28.txt > FISSEQRT_bowtie2_totRNA.sam 7024 reads; of these: 7024 (100.00%) were unpaired; of these: 4574 (65.12%) aligned 0 times 2447 (34.84%) aligned exactly 1 time 3 (0.04%) aligned >1 times 34.88% overall alignment rate mzcai@genome-miner:~/scratch/RanHex_EnrichmRNA/inVitroRTSeq$ bowtie2 --phred64 -x ~/scratch/RanHex_EnrichmRNA/tot_rRNA -q s_1_1_Indx29.txt > Top48_bowtie2_totRNA.sam 12158 reads; of these: 12158 (100.00%) were unpaired; of these: 7388 (60.77%) aligned 0 times 4764 (39.18%) aligned exactly 1 time 6 (0.05%) aligned >1 times 39.23% overall alignment rate mzcai@genome-miner:~/scratch/RanHex_EnrichmRNA/inVitroRTSeq$ bowtie2 --phred64 -x ~/scratch/RanHex_EnrichmRNA/tot_rRNA -q s_1_1_Indx32.txt > gDNA_bowtie2_totRNA.sam 111950 reads; of these: 111950 (100.00%) were unpaired; of these: 111132 (99.27%) aligned 0 times 817 (0.73%) aligned exactly 1 time 1 (0.00%) aligned >1 times 0.73% overall alignment rate *RanHex: 45.52% (5,441 reads) *dT: 16.36% (10,905 reads) *FISSEQRT: 34.88% (7,024 reads) *Top48: 39.23% (12,158 reads) *gDNA: 0.73% (111,950 reads)
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