Question: No Sequence In Fastq File That Was Converted From Ncbi Sra File
0
gravatar for ferris.us
3.9 years ago by
ferris.us20
ferris.us20 wrote:

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

ncbi sra fastq sequence • 1.6k views
ADD COMMENTlink modified 3.9 years ago by Neilfws47k • written 3.9 years ago by ferris.us20
1
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan74k
Freiburg, Germany
Devon Ryan74k wrote:

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.

ADD COMMENTlink written 3.9 years ago by Devon Ryan74k

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

ADD REPLYlink written 3.9 years ago by ferris.us20

Tophat with bowtie1 should work.

ADD REPLYlink written 3.9 years ago by Devon Ryan74k
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