I recently started working with RNA seq analysis and despite having some expertise in R, I'm very new in the linux environment! I've been trying to analyze miRNA seq data (illumina) from a human cell line and I've not been very lucky. My sequences are about 50 nucleotides long and my workflow has been: adapter removal (cutadapt), mapping with both bowtie and bowtie2 (i'm using Homo_sapiens.GRCh38.ncrna.fa as a reference genome in this step) and finally HTseq-count, trying both GRCh38.p13_genomic.gff.gz and Homo_sapiens.GRCh38.99.gtf.gz reference genome. Although my alignment results from bowtie is showing around 25% of mapping, all my htseq results only give me 0 counts. Am I using the wrong reference genome for aligning or counting (or both)? Any suggestion? Thank you!
Question: small RNA seq data from human cell line only give me 0 counts
8 months ago by
leandroteixeira • 0
leandroteixeira • 0 wrote:
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