2.Expression Matrix
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File format
Information contained in file
File description
Notes
bam
alignments
Produced by mapping reads to the transcriptome.
Reads are trimmed using a proprietary version of cutAdapt. We map to transcriptome for a better sensitivity (see details in protocol and example).
File format
Information contained in file
File description
Notes
bigWig
signal
Normalized RNA-seq signal
Signals are generated for transcriptome both the plus and minus strands and for unique reads and unique+multimapping reads.
tsv
gene (ncRNA) quantifications
Non-normalized counts.
RSEM
homer
HTseq
FeatureCounts
Visualize your mapped reads with IGV (locally) and/or UCSC Genome Browser (on line).
Learn how to construct the expression matrix using HTSeq, featureCounts and homer; then compare the difference among these three methods.
Bioinformatics Data Skills
11) Working with Alignment Data
: 2. Construction of expression matrix