basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file: dm3 (Release 5) and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file (.xlsx)

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file:dm3 and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking:

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file:dm3 and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking:

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file:dm3 and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking:

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file:dm3 and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking:

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file: dm3 (Release 5) and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file (.xlsx)

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file:dm3 and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking:

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file: dm3 (Release 5) and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file (.xlsx)

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file:dm3 and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking:

basecalling: CASAVA v1.8.2reads aligned to genome using Bowtie2 v 2.0.6identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtfcalculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtfGenome_build: Refseq annotation file:dm3 and dm3-iGenomes.gtfSupplementary_files_format_and_content: Cufflinks output file: genes.fpkm_tracking: