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==Comparison of CA12k to Agi26k Results Summary== {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''CA12k''' | align="center" style="background:#f0f0f0;"|'''Agi26k0gap''' | align="center" style="background:#f0f0f0;"|'''Agi26k20gap''' |- | Good probes|| 7,900 || 6,596 || 5,403 |- | Good genes|| 3,141 || 2,628 || 2,529 |- | Brain-optimized probes|| 6,412 || 8,640 || 8,438 |- | Brain-optimized genes|| 2,615 || 3,140 || 3,133 |- | Good & Brain-optimized probes|| 4,185 || 4,822 || 4,006 |- | Good & Brain-optimized genes|| 1,963 || 2,075 || 2,075 |- | Good & Brain-optimized brain genes|| 1,849 || 2,002 || 1,996 |- | Good & Brain-optimized stem cell genes|| 189 || 138 || 151 |} <!-- 1. Starting with 3 R1_001.fastq MiSeq reads clip the reads to the first 46 nt with h1h2_first46_only.pl 2. Run each of the 3 46shortened.fastq files through Bowtie2 * ./bowtie2 -k 1 --phred33 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /media/Ext12T/GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/Bowtie2Index/genome -q /home/kunzhang/seqStore/130325_MiSeq/gDNA_R1_46shortened.fastq > /home/kunzhang/seqStore/130325_MiSeq/gDNA_outputv4.txt 4476041 reads; of these: 4476041 (100.00%) were unpaired; of these: 180684 (4.04%) aligned 0 times 4295357 (95.96%) aligned exactly 1 time 0 (0.00%) aligned >1 times 95.96% overall alignment rate * ./bowtie2 -k 1 --phred33 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /media/Ext12T/GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/Bowtie2Index/genome -q /home/kunzhang/seqStore/130325_MiSeq/cDNA-RNaseA_R1_46shortened.fastq > /home/kunzhang/seqStore/130325_MiSeq/cDNA-RNaseA_outputv4.txt 2852904 reads; of these: 2852904 (100.00%) were unpaired; of these: 132404 (4.64%) aligned 0 times 2720500 (95.36%) aligned exactly 1 time 0 (0.00%) aligned >1 times 95.36% overall alignment rate * ./bowtie2 -k 1 --phred33 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /media/Ext12T/GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/Bowtie2Index/genome -q /home/kunzhang/seqStore/130325_MiSeq/cDNAwRNaseA_R1_46shortened.fastq > /home/kunzhang/seqStore/130325_MiSeq/cDNAwRNaseA_outputv4.txt 2091417 reads; of these: 2091417 (100.00%) were unpaired; of these: 99778 (4.77%) aligned 0 times 1991639 (95.23%) aligned exactly 1 time 0 (0.00%) aligned >1 times 95.23% overall alignment rate 3. Turn 200bp ordered probe oligo sequences into CAprobes.fastq and run through Bowtie2 to get probes_output.txt * ./bowtie2 -k 1 --phred33 --mp 1,0 --rdg 0,1 --rfg 0,1 -x /media/Ext12T/GenomeDB/UCSC/Homo_sapiens/hg19/Sequence/Bowtie2Index/genome -q /home/kunzhang/seqStore/130325_MiSeq/CAprobes.fastq > /home/kunzhang/seqStore/130325_MiSeq/probes_output.txt 12355 reads; of these: 12355 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 12355 (100.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 100.00% overall alignment rate 4. Count reads for each probe by matching the alignments in outputv4.txt (SAM files) to probes_output.txt * Count_reads_from_bowtie2_SAM_gDNA.pl (536,927 reads not matched) * Count_reads_from_bowtie2_SAM_cDNA-RNaseA.pl (222,592 reads not matched) * Count_reads_from_bowtie2_SAM_cDNAwRNaseA.pl (164,310 reads not matched) [[Media:FilteringGoodProbes_matched_to_Genes.xlsx|Counts matched with probes from:]] *[[Media:probe2padlockFISSEQ_Feb2013_0bp.txt|probe2padlockFISSEQ_Feb2013_0bp.pl]] [[Media:probe2padlockFISSEQ_Feb2013_0bp_stemCellGenes.txt|probe2padlockFISSEQ_Feb2013_0bp_stemCellGenes.pl]] *Also has filtered probes leaving: **"good" probes (gDNA count between 100 and 1000) **Brain optimized probes (cDNA-RNaseA count between 10 and 1000 or just greater than 10) 5. Plot the counts <br/> [[File:InSitu_MiSeq_CAgoodprobes.jpg]] [[File:InSitu_MiSeq_CAbrainoptimizedprobes.jpg]] [[File:InSitu_MiSeq_CAcDNA_vs_cDNA.jpg]] 6. Summarize results *"Good" probes have gDNA counts between 100 and 1000 **7,736 "good" probes from 12,355 total **3,099 unique genes *Brain optimized probes are "good" probes that also have cDNA-RNaseA counts between 10 and 1000 **5,270 brain optimized probes from 12,355 total **1,619 unique genes [[Media:CustomArray_Probe_Analysis_Summaryv4.docx|Final Summary]]-->
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