Hello everyone! I am a newbie for microbiome analysis. So I tried to practice general Metatranscriptomics
analysis using the pipeline (1.Kneaddata, 2. Metaphlan3/HUMAnN/ or possible Kraken). But after I used Kneaddata, its output is weird. What have I missed?
First of all, I downloaded SRR769427 using faster-dump. More detailed information is belowed
Since it is human gut metatranscriptome,1) I downloaded DB using [$ kneaddata_database --download human_transcriptome bowtie2 $DIR]
then 2) [kneaddata -i SRR769427_1.fastq --i SRR769427_2.fastq --reference-db $DATABASE --output $OUTPUT_DIR --trimmomatic $TRIM_DIR]
then my outputs are
The Kneaddata menual for pairends data says SRR***.kneaddata_paired_1.fastq and SRR***.kneaddata_paired_2.fastq are final outputs. But volume of mine are zero.
Could you help me out what have I done wrong?
My question is
- Since the files that I want to analyze are human transcripomic data, shoud I use human transcriptome data as a DB in bowtie2 for removing human mRNA for metatranscriptome analysis ?
Many thankx in advance