Question: Confusion in SRA submission
0
gravatar for arunprasanna83
16 months ago by
arunprasanna8330 wrote:

Hello,

I am downloading an SRA data for a study. The study is basically, Illumina Paired data. However, the study description shows that, "This run has 2 reads per spot" and Reads section show the following:

Reads (separated)

>gnl|SRA|SRR768721.1.1 HWI-ST0798_0099:2:1101:1545:2240 (Biological) CCAGAATGCGCCCGGTGCATTCTGGGACTCCGAATCAGAAGAGGGAGTTGCGTCAGAGGC GGAGGTGGATGAAGCAGCGGGAGGAGAGGCGGAATCATCGG

>gnl|SRA|SRR768721.1.2 HWI-ST0798_0099:2:1101:1545:2240 (Biological) TACACTCGTAACCTCCTCGCCGCCAACCCCGACGTTCTTCAAGAGGGTGGTGCCATTGAC CTAAGCTCAATGTCCAGCNCNNNNNNNNNNNNNNNNNNNNN

Does this mean that, .1 & .2 represent the pairs and I should 'fastq-dump --split-files' to split them into two files ?

Thanks in Advance,

AP

rna-seq sra • 558 views
ADD COMMENTlink modified 16 months ago by genomax55k • written 16 months ago by arunprasanna8330
2
gravatar for genomax
16 months ago by
genomax55k
United States
genomax55k wrote:

That is correct. I suggest you make your task easy and download the fastq files from ENA here. No sratoolkit needed.

ADD COMMENTlink written 16 months ago by genomax55k

Wow. Thats cool ! I didn't know about this !

ADD REPLYlink written 16 months ago by arunprasanna8330

Always check ENA to see if fastq's are available. They generally are except for recent SRA submissions (which eventually appear).

ADD REPLYlink modified 16 months ago • written 16 months ago by genomax55k
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