Conversion of Fastq.gz to text file

Question

[Ahmad_Bio]

Hi,

I am new to bioinformatics, so would like to ask basic questions. I received data in fastq.gz format (Illumina data, R1 and R2 files). How can I convert this to *.txt format using some tools to visualize reads.

Furthermore, can someone recommend guideline, how to utilize fastq files for further analysis, removing barcodes, join paired ends, picking OTUs.

Thank you community,

Answer 1

[EagleEye]

You question is not clear. First of all why do you want to visualize FASTQ files? What are these samples RNAseq, DNA, exome etc? Each follows different bioinformatics pipelines.

If you want to check the file over command line use this on your Linux terminal,

zcat input.fq.gz | head

Most of the quality control tools and aligners support FASTQ files as compressed formats such as .gz. If you still want your file as plain text format (uncompressed, takes lot of space some time 10 times to your compressed file). The following is the Linux command to uncompress .gz files,

gunzip -d input.fastq.gz

Information about FASTQ files.

What do you mean by join paired-ends?

This is one of the available bioinformatics protocol for rnaseq, you can try these steps (if RNAseq),

A: Any One please provide protocol for Analysing long noncoding RNA illumina NGS da

After alignment step (3rd) the BAM/SAM files will be generated and you can use browsers like IGV to visualize your mapped reads from bam files.

Information about BAM/SAM file format.