Basecalls performed using CASAVA version v1.8.2 Trimmed reads with fastx_quality_trimmer 0.0.13 with a quality treshhold of 18 and a length of 20 Aligned with Bowtie 2.1.0 and Tophat 2.0.10 using Gencode v19 junctions Samtools 0.1.19-44428cd to make a bam, sort, index Raw counts were generated using htseq_count 0.6.1 using the UCSC HG19 known gene transcripts from Illumina iGenomes edgeR 3.2.4 in R 3.1.0 were used to normalize counts between samples and to make comparisons between groups. Genome_build: hg19 Supplementary_files_format_and_content: Normalized reads in CPM for each detected gene along with differential gene expression log2 (fold change) and p-values for each time point
This is the data processing detail for a paper. I downloaded fastq files from this paper and used STAR alignment and featureCounts to get my read matrix with the reference of Homo_sapiens.GRCh38 from ENSEMBL. However, with featureCounts, only 3% reads were aligned. (This is single-end fastq file so I used -s 0, -s 1, -s 2 option for featureCounts but all results were bad) What went wrong with my pipeline? Is it related to reference genome that I used?