Hi everyone,
I have fastq files from Illumina small RNA-Seq. My first goal is to analyze differential expression of known miRNAs.
I trimmed the adapter 3' with cutadapt and mapped the reads with Bowtie. I'm running htseq-count with the hsa.gff3 file from miRBase, but I get 0 counts per miRNA.
I don't understand what I am doing wrong. I need some help.
Thanks a lot!
I used these commands:
I have fastq files from Illumina small RNA-Seq. My first goal is to analyze differential expression of known miRNAs.
I trimmed the adapter 3' with cutadapt and mapped the reads with Bowtie. I'm running htseq-count with the hsa.gff3 file from miRBase, but I get 0 counts per miRNA.
I don't understand what I am doing wrong. I need some help.
Thanks a lot!
I used these commands:
Code:
bowtie --sam -n 0 -l 15 -e 99999 -k 100 --best --chunkmbs 128 Reference_genome/h_sapiens_37_asm.ebwt/h_sapiens_37_asm reads_trimmed.fasq > aligned.sam
Code:
htseq-count -m union -t miRNA -s yes -i Name aligned.sam miRBase/genomes/hsa.gff3
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