fastq-dump on SRA files

harlock0083 · 07-06-2011, 11:50 AM

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 · 07-06-2011, 10:33 PM

All of the mentioned runs are fragments - single read

ndeshpan · 07-06-2011, 11:06 PM

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 · 07-07-2011, 12:12 AM

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 · 07-07-2011, 12:30 AM

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 · 07-07-2011, 06:41 AM

Quote:

Originally Posted by srasdk

All of the mentioned runs are fragments - single read

Thank you for the reply.

ndeshpan · 07-08-2011, 08:04 PM

Thanks everyone

afkoeppel · 07-12-2011, 08:10 AM

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 · 07-20-2011, 09:27 AM

Try fastq-dump -SL

afkoeppel · 07-20-2011, 11:30 AM

Quote:

Originally Posted by Benjamin Vincent

Try fastq-dump -SL

This did the trick. Thank you very much.

hithesh · 12-01-2015, 10:34 PM

use this command

open SRA toolkit kit path

open bin folder

fastq-dump.exe pathfile\filename outputfilename

Tlexander · 10-31-2016, 09:37 AM

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

yasbo · 09-20-2018, 12:03 AM

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 · 10-18-2018, 02:13 AM

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 · 10-18-2018, 04:19 AM

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.

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07-06-2011, 11:50 AM	#1
harlock0083 Member Location: evanston Join Date: Jul 2011 Posts: 15	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?

12-01-2015, 10:34 PM	#11
hithesh Junior Member Location: bengaluru Join Date: Nov 2015 Posts: 1	To Convert SRA to Fastq use this command open SRA toolkit kit path open bin folder fastq-dump.exe pathfile\filename outputfilename

10-18-2018, 02:13 AM	#14
fraurelie Junior Member Location: uk Join Date: Oct 2018 Posts: 1	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?

07-06-2011, 10:33 PM	#2
srasdk Member Location: Maryland, USA Join Date: Jun 2011 Posts: 19	All of the mentioned runs are fragments - single read

07-06-2011, 11:06 PM	#3
ndeshpan Member Location: Sydney Join Date: Nov 2009 Posts: 29	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

07-07-2011, 12:12 AM	#4
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	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.

07-07-2011, 12:30 AM	#5
srasdk Member Location: Maryland, USA Join Date: Jun 2011 Posts: 19	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'

07-08-2011, 08:04 PM	#7
ndeshpan Member Location: Sydney Join Date: Nov 2009 Posts: 29	Thanks everyone

07-12-2011, 08:10 AM	#8
afkoeppel Member Location: VA Join Date: Jul 2011 Posts: 17	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?

07-20-2011, 09:27 AM	#9
Benjamin Vincent Junior Member Location: USA Join Date: Jul 2011 Posts: 2	Try fastq-dump -SL

10-31-2016, 09:37 AM	#12
Tlexander Member Location: china shanghai Join Date: Aug 2010 Posts: 14	fastq-dump --split-files --gzip ./SRR1232309.sra

09-20-2018, 12:03 AM	#13
yasbo Junior Member Location: israel Join Date: Sep 2018 Posts: 1	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

10-18-2018, 04:19 AM	#15
ddb Member Location: Europe Join Date: Feb 2012 Posts: 13	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.