alias: A375m291
title: A375_mimic_miR29a_1
design: Base-calling: Original image data file from high-throughput sequencing is transformed into Raw Reads by CASAVA base recognition. Filtering: (1)Remove reads with adaptor contamination.  (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5. Alignement: STAR software is used to accomplish the mapping. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads. HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
identifiers.namespace: SUB7273127
identifiers.id: A375m291