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===Building bowtie2 index for Agi26k probes=== *For 0gap probes converted probelist to fasta file with H1, H2,and barcode region rearranged similar to CA12kprobes [[Media:Agi26k0gapProbelist_to_fasta.txt | Agi26k0gapProbelist_to_fasta.pl]]: FISSEQ_Probes_Dec2012.txt -> Agi26k0gapprobes_to_order_H1H2.fa **Fasta reference made to match reads: RevComp(H1) + RevComp(H2) + RevComp(Barcode) **Had to delete probes 12964-26142 since they are 20gap probes *For 20gap probes did something similar but had to include 20bp target region in between H1 and H2 [[Media:Agi26k20gapProbelist_to_fasta_corrected.txt | Agi26k20gapProbelist_to_fasta_corrected.pl]]: FISSEQ_Probes_Dec2012.txt -> Agi26k20gapprobes_to_order_H1H2_corrected.fa **Target sequence was found by using H1 sequence to search through outputFile_20gap.txt and outputFile_20gap_stem.txt (the two files output from ppDesigner when designing probes for genes and stem cell genes) **Fasta reference made to match reads: RevComp(H1) + target + RevComp(H2) + RevComp(Barcode) **Had to delete probes 0-12963 since they are 0gap probes *Build index: genome-miner:$ bowtie2-build Agi26k0gapprobes_to_order_H1H2.fa Agi26k0gap_H1H2 genome-miner:$ bowtie2-build Agi26k20gapprobes_to_order_H1H2_corrected.fa Agi26k20gap_H1targetH2
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