I Did Not Get Output File When I Ran Fastx_Toolkit

Question

[Raghav]

hello you all, I have query regarding quality check of fastq file. I have fastq file of paired end reads generated by illumina sequencing. I tried to map my fastq to reference without checking quality of the fastq file and encountered an error during SAM to BAM conversion. Now I find list of tools which help me check quality of fastq file which are fastx , fastQC and HTQC, i randomly selected fastx to check quality of my fastq file by using syntax

fastx_quality_stats -N -i /storage/home/cdac/raghav/sratoolkit.2.3.2-4-centos_linux64/bin/SRR681003.fastq -o SRR681003

I am getting my output with zero KB size, I am getting my out put without any information, please kindly help me out.

how we do decide the good quality reads and bad quality reads??? how do we filter bad quality reads by using particular syntax??

your valuable comments and suggestions are always welcome.

[Sukhi Singh]

add -Q33 in the command, see if that helps !!

Answer 1

[Joseph Hughes]

Open your fastq read file in fastQC and you will get a nice visualization of the quality of your reads as well as the particular fastq format used which you can then use to do you quality filtering.