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Old 07-06-2011, 10:50 AM   #1
harlock0083
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Default fastq-dump on SRA files

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?
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Old 07-06-2011, 09:33 PM   #2
srasdk
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All of the mentioned runs are fragments - single read
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Old 07-06-2011, 10:06 PM   #3
ndeshpan
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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
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Old 07-06-2011, 11:12 PM   #4
simonandrews
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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.
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Old 07-06-2011, 11:30 PM   #5
srasdk
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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'
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Old 07-07-2011, 05:41 AM   #6
harlock0083
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Quote:
Originally Posted by srasdk View Post
All of the mentioned runs are fragments - single read
Thank you for the reply.
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Old 07-08-2011, 07:04 PM   #7
ndeshpan
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Thanks everyone
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Old 07-12-2011, 07:10 AM   #8
afkoeppel
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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?
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Old 07-20-2011, 08:27 AM   #9
Benjamin Vincent
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Try fastq-dump -SL
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Old 07-20-2011, 10:30 AM   #10
afkoeppel
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Quote:
Originally Posted by Benjamin Vincent View Post
Try fastq-dump -SL
This did the trick. Thank you very much.
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Old 12-01-2015, 09:34 PM   #11
hithesh
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Default To Convert SRA to Fastq

use this command

open SRA toolkit kit path

open bin folder

fastq-dump.exe pathfile\filename outputfilename
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Old 10-31-2016, 08:37 AM   #12
Tlexander
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fastq-dump --split-files --gzip ./SRR1232309.sra
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Old 09-19-2018, 11:03 PM   #13
yasbo
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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
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