fastq-dump on SRA files

[harlock0083]

Hello, I have a question about .sra files.
I've downloaded the .sra files from this dataset.

SRR039628.sra
SRR039629.sra
SRR039630.sra
SRR039631.sra
SRR039632.sra
SRR039633.sra

However, after running

./fastq-dump -A SRR039628 SRR039628.sra

I only get 1 file: SRR039628.fastq. I thought on paired end reads I would get 3 files SRR039628_1.fastq and SRR039628_2.fastq along with SRR039628.fastq. Am I doing something wrong?

[srasdk]

All of the mentioned runs are fragments - single read

[ndeshpan]

hi,

I have downloaded a file from SRA and used fastq-dump..

However when I check my output .fastq file I see this



head -10 SRR036210.fastq
@SRR036210.1 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_144 length=25
T2030201230313112312001111
+SRR036210.1 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_144 length=25
!"""""""""""""""""""""""""
@SRR036210.2 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_198 length=25
T2030201230313112312001111
+SRR036210.2 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_198 length=25
!"""""""""""""""""""""""""
@SRR036210.3 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_1360 length=25
T2030201230313112312001111


Any suggestions?

cheers,

Nandan

[simonandrews]

That's a colorspace fastq file. From the bit you posted it looks OK, but you'll need to use colorspace aware tools to do anything with it.

[srasdk]

fastq-dump defaults to colorspace for SOLiD technology.
You can use '-B' option to force translation into basespace if you wish - the only downside - all bases after miscalled color '.' will become 'N'

[harlock0083]

All of the mentioned runs are fragments - single read

Thank you for the reply.

[ndeshpan]

Thanks everyone

[afkoeppel]

I'm having the same basic problem as the original poster in this thread.
I downloaded the file: SRR063783.sra, and ran fastq-dump on it.

It's supposed to be paired-end data, but I'm only getting a single file: SRR063783.fastq

In this file it looks as though each pair of forward and reverse reads has been combined into a single sequence. Is there a way to split them up again?

[Benjamin Vincent]

Try fastq-dump -SL

[afkoeppel]

Try fastq-dump -SL

This did the trick. Thank you very much.

[hithesh]

To Convert SRA to Fastq

use this command

open SRA toolkit kit path

open bin folder

fastq-dump.exe pathfile\filename outputfilename

[Tlexander]

fastq-dump --split-files --gzip ./SRR1232309.sra

[yasbo]

Hi,
Been using fasterq-dump.2 to download and save fastq files.
How can I download the fastq files using fasterq-dump and still keep original read names with details about each read as seen on ncbi website?

site: https://www.ncbi.nlm.nih.gov/sra

[fraurelie]

Converting SRA files into Fastq

Hi I am new to bioinformatics I did some courses online and loved it which doesn't mean I find it easy! On the contrary and I really admire you guys who can get around it!

First step, I want to get SRR7962225 as fastq format.

I downloaded the data sra_data.fastq.gz and the SRA toolkit but it refuses to convert it using fastq-dump however I get something like

2·43222Õ3Ô3T0TÈIÍK/É°540ä ÿÿ,ŒÁ......etc

using Notepad.

Any suggestions?

[ddb]

Some more details about the commands you have run would be helpful. If the file has a .gz extension then it needs to be unzipped first. I may be wrong but it sounds like you are on a windows os so try 7zip to decompress. Depending on your objective you might be limited on the analyses you can perform on windows os.