zcat CTG_pH7.1-GSM1470703/SRR1542931_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o CTG_pH7.1-GSM1470703/SRR1542931.circ_35bp.v0.a.bowtie.bam
zcat CTG_pH7.2-GSM1470704/SRR1542932_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o CTG_pH7.2-GSM1470704/SRR1542932.circ_35bp.v0.a.bowtie.bam
zcat CTG_pH7.3-GSM1470705/SRR1542933_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o CTG_pH7.3-GSM1470705/SRR1542933.circ_35bp.v0.a.bowtie.bam
zcat CTG_pH8.1-GSM1470706/SRR1542934_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o CTG_pH8.1-GSM1470706/SRR1542934.circ_35bp.v0.a.bowtie.bam
zcat CTG_pH8.2-GSM1470707/SRR1542935_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o CTG_pH8.2-GSM1470707/SRR1542935.circ_35bp.v0.a.bowtie.bam
zcat CTG_pH8.3-GSM1470708/SRR1542936_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o CTG_pH8.3-GSM1470708/SRR1542936.circ_35bp.v0.a.bowtie.bam
zcat PLK_pH7.1-GSM1470697/SRR1542925_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o PLK_pH7.1-GSM1470697/SRR1542925.circ_35bp.v0.a.bowtie.bam
zcat PLK_pH7.2-GSM1470698/SRR1542926_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o PLK_pH7.2-GSM1470698/SRR1542926.circ_35bp.v0.a.bowtie.bam
zcat PLK_pH7.3-GSM1470699/SRR1542927_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o PLK_pH7.3-GSM1470699/SRR1542927.circ_35bp.v0.a.bowtie.bam
zcat PLK_pH8.1-GSM1470700/SRR1542928_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o PLK_pH8.1-GSM1470700/SRR1542928.circ_35bp.v0.a.bowtie.bam
zcat PLK_pH8.2-GSM1470701/SRR1542929_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o PLK_pH8.2-GSM1470701/SRR1542929.circ_35bp.v0.a.bowtie.bam
zcat PLK_pH8.3-GSM1470702/SRR1542930_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o PLK_pH8.3-GSM1470702/SRR1542930.circ_35bp.v0.a.bowtie.bam
zcat RH_pH7.1-GSM1470691/SRR1542919_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o RH_pH7.1-GSM1470691/SRR1542919.circ_35bp.v0.a.bowtie.bam
zcat RH_pH7.2-GSM1470692/SRR1542920_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o RH_pH7.2-GSM1470692/SRR1542920.circ_35bp.v0.a.bowtie.bam
zcat RH_pH7.3-GSM1470693/SRR1542921_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o RH_pH7.3-GSM1470693/SRR1542921.circ_35bp.v0.a.bowtie.bam
zcat RH_pH8.1-GSM1470694/SRR1542922_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o RH_pH8.1-GSM1470694/SRR1542922.circ_35bp.v0.a.bowtie.bam
zcat RH_pH8.2-GSM1470695/SRR1542923_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o RH_pH8.2-GSM1470695/SRR1542923.circ_35bp.v0.a.bowtie.bam
zcat RH_pH8.3-GSM1470696/SRR1542924_1.fastq.gz | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.CS -p 1 -v 0 -C --chunkmbs 2000 -a -t --best --strata -q --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Apicomplexa/Toxoplasma_gondii/circ_RNA/Toxoplasma_gondii.ToxoDB-7.1.20.annotation+circular_junctions_35mers.fa - -o RH_pH8.3-GSM1470696/SRR1542924.circ_35bp.v0.a.bowtie.bam