No Sequence In Fastq File That Was Converted From Ncbi Sra File

Question

[ferris.us]

I have downloaded some SRA from NCBI which are SRR486147, SRR486148, SRR486149, SRR486150, SRR486151, SRR486214 and SRR486215. I also converted them to fastq files by using SRA Toolkit (fastq-dump --split-files SRR486147.sra). However the fastq files that were generated are not as usual. There are no sequences in the files. Are they correct? You can see a picture from the address below. Thanks!

https://lh3.googleusercontent.com/-QUGQEn1BCXo/UxLRKTL7h8I/AAAAAAAAAxo/5W4HAlvTKak/w796-h335-no/SRR496619.jpg

Answer 1

[Devon Ryan]

Those are fastq files, it's just that they're color space rather than standard. Here's a blog post I found regarding converting the two.

[ferris.us]

Thanks for pointing it out! Do you know which tool is good for alignment? Can I use Tophat and bowtie2?

[Devon Ryan]

Tophat with bowtie1 should work.