Thank you GenoMax. That worked perfectly. So whatever I name the bowtie1/2 index database should be the name used for the database location at the end. I will definitely remember that.
I have tested two sets out. In my first set, I know sequence belongs to what I am providing for the database, but I get everything as Unmapped. This is strange, is there I am doing something wrong?
The bowtie1/2 index were made using bowtie-build of the reference genome found on NCBI.
In other sample, there was an Arabidopsis contamination (somewhere between 2 to 0.2%) and I am trying to remove the regions that are not infected by using the --nohits option.
The same thing occurred with everything came back as Unmapped, which is strange.
Should be good version:
Contamination version:
Any ideas what is occurring and why is everything coming back unmapped?
EDIT: Is there method to filter out reads that actually match to a certain genome/s as one or separate files (paired end or single end reads- fastq).
I have tested two sets out. In my first set, I know sequence belongs to what I am providing for the database, but I get everything as Unmapped. This is strange, is there I am doing something wrong?
The bowtie1/2 index were made using bowtie-build of the reference genome found on NCBI.
In other sample, there was an Arabidopsis contamination (somewhere between 2 to 0.2%) and I am trying to remove the regions that are not infected by using the --nohits option.
The same thing occurred with everything came back as Unmapped, which is strange.
Should be good version:
Code:
fastq_screen --threads 8 --aligner bowtie2 --conf=/Users/ZainA/Downloads/Dmel_520/Dmel5_20.conf --paired /Users/ZainA/Downloads/Dmel_520/forward.fastq /Users/ZainA/Downloads/Dmel_520/reverse.fastq --outdir Output
Code:
fastq_screen --threads 8 --aligner bowtie2 --conf=/Users/ZainA/Downloads/Dmel_520/Arabidopsis/Arabidopsis_gnomon_mRNA.conf --paired /Users/ZainA/Downloads/Dmel_520/Arabidopsis/forward_1p3.fastq /Users/ZainA/Downloads/Dmel_520/Arabidopsis/reverse_2p3.fastq --nohits --outdir output
EDIT: Is there method to filter out reads that actually match to a certain genome/s as one or separate files (paired end or single end reads- fastq).
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