Entering edit mode
16 months ago
eimanpharmacist
▴
20
Hi,
I am new to using trinity tool, and I went through a tutorial to run and assess the assembly.
I already generated Trinity.fasta file, then # Build Index using this:
bowtie2-build ~/workdir/trinity/trinity_out_dir/Trinity.fasta index/Trinity.fa
This generated multiple Trinity.fa files in the index folder
bowtie2_assessment/index$ ls
Trinity.fa.1.bt2 Trinity.fa.3.bt2 Trinity.fa.rev.1.bt2
Trinity.fa.2.bt2 Trinity.fa.4.bt2 Trinity.fa.rev.2.bt2
So, when I ran
R1="$HOME/workdir/sample_data/sample1-ErccTranscripts-chr22.read1.fastq.gz"
R2="$HOME/workdir/sample_data/sample2-ErccTranscripts-chr22.read2.fastq.gz"
bowtie2 -p 1 -q --no-unal -k 20 -x index/Trinity.fa -1 $R1 -2 $R2 2> align_stats.txt| samtools view -Sb -o bowtie2.bam
# View align_stats.txt
cat align_stats.txt
I got this error message:
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
since I do not have Trinity.fa, but multiple Trinity.fa files.
I do not understand what is wrong here. Your help is much appreciated!
Did the process complete successfully?
It is completed but I can not find any bam files, as you see above, I should get a bowtie2.bam file as an output but I did not.
I think the problem in bowtie2 installation. it was installed using this:
conda install -c bioconda bowtie2
I removed it then re-installed usingBut now, it generates a new error (command bowtie2 does not exit. I also tried
sudo apt install bowtie2
Same output