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

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

fastq ncbi sra sequence
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updated by Neilfws Neilfws • written by ferris.us • ferris.us

1 answer

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.

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written by Devon Ryan Devon Ryan

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

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written by ferris.us • ferris.us

Tophat with bowtie1 should work.

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written by Devon Ryan Devon Ryan

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