Question: prefetch and fast-dump problems?
0
gravatar for debitboro
7 days ago by
debitboro190
Belgium
debitboro190 wrote:

Dear all,

I want to download some SRR files, and then convert them to fastq files. For that, I've used the following SRA-toolkit commands:

prefetch SRR3159525
fastq-dump SRR3159525.sra

The download was done successfully, and the size of the resulted fastq file seems correct (~8G).

But when I've checked the content of the fastq file, I found the file was strangely formatted as follows:

 @SRR3159522.1 2_33_78 length=50
 T..................................................G
 +SRR3159522.1 2_33_78 length=50
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 @SRR3159522.2 2_36_51 length=50
 T..................................................G
 +SRR3159522.2 2_36_51 length=50
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 @SRR3159522.3 2_39_77 length=50
 T30.0..2.0.....2.2..2.0..0......0....1...220.2.3322G
 +SRR3159522.3 2_39_77 length=50
 !(*!%!!(!%!!!!!%!%!!%!&!!%!!!!!!*!!!!&!!!%%*!%!&%'%!
 @SRR3159522.4 2_39_134 length=50
 T01.0..0.1.....2.0..2.2..2......1....1...231.0.3312G
 +SRR3159522.4 2_39_134 length=50
 !1&!(!!&!.!!!!!%!(!!%!%!!)!!!!!!)!!!!%!!!%%(!%!/)%%!
 ...
 ...

As you can see, the sequence of the reads contains integers delimited by T and G?

Thank you for your help in advance

ADD COMMENTlink written 7 days ago by debitboro190
0
gravatar for GenoMax
7 days ago by
GenoMax96k
United States
GenoMax96k wrote:

There is something weird with this submission. Initial reads are odd looking as you posted while some of the later ones look like

>gnl|SRA|SRR3159525.999995.1 60_1827_793 F3 (Biological)
ACGCATGCCTGCTGTAGTCAATTAAGTACACAAACTGACATCCANNNNNN
>gnl|SRA|SRR3159525.999995.2 60_1827_793 (Biological)
Empty read

Looks like Read1 = 50 is somewhat OK, Read 2 = 35 bp is empty :-(

Contact SRA support to see if they have anything to say.

ADD COMMENTlink modified 7 days ago • written 7 days ago by GenoMax96k
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