P-GSE24178-7 - P-GSE24178-7
***fastq*** Image analysis, base calling, quality filtering: Standard settings of GAPipeline 1.3+ using PhiX control; Fastq files contain full length reads (36nts) that passed the chastity filter. If necessary, quality scales were adjusted to phred64. ***bam format alignment*** Illumina reads in fastq format were aligned against the mouse mm9 genome with bowtie 0.12.5 using parameters '--phred64-quals --chunkmbs 128 --all -m 1 --best --strata -l 36 -p8 --sam'. Sam files were converted to bam, unmapped reads were removed, and bam files were sorted with samtools 0.1.12.