Is It Fastq Format

Question

[vigneshnivas09]

i have sra 720007.sra file dataset, which neither I can convert to Fastq. how to dataset convert to fastq format this data?

Answer 1

[Matt Shirley]

It seems like you might need some basic Linux training. I suggest starting with the lessons at software carpentry. For now, however, I have a suggestion: why don't you try your task using Galaxy? I wrote the initial version of the SRA toolkit Galaxy integration that's now on the public server. You should be able to play around with your data now, while learning the Linux basics you need to go further with your analysis.

Answer 2

[Michael]

No, it is not fastq format. For handling Sequence read archive (SRA) files, please refer to https://ncbi.github.io/sra-tools/

[vigneshnivas09]

sry SRR1740401.sra SRR1740403.sra this file iam using ubuntu software . any manual for this dataset?

[firatuyulur]

go to https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software and click on ubuntu linux 64 bit architecture. save the file. then open a folder called "sratoolkit" in your home directory. move your .tar.gz file into your sratoolkit directory. then open a terminal in sratoolkit direcotry. type tar xzvf sratoolkit.2.8.1-ubuntu64.tar.gz. then type export PATH=$PATH:/home/.your.path.to.sratoolkit.directory./sratoolkit/sratoolkit.2.8.1-ubuntu64/bin in your terminal. now you will be able to use sratoolkit tools from your terminal. type " fastq-dump SRR1740401" . this will take time to finish its job.

[vigneshnivas09]

`export PATH=$PATH:/home/.your.path.to.sratoolkit.directory./sratoolkit/sratoolkit.2.8.1-ubuntu64/bin`
-bash: export PATH=/opt/rh/python27/root/usr/bin:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/share/apps/amber14/bin:/usr/R-3.0.2/bin:/usr/local/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/mpich2/gnu/bin/:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/maven/bin:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/condor/bin:/opt/condor/sbin:/share/apps/mpich-ib/bin:/share/apps/python/python-2.7.11/bin:/share/apps/python/python-3.5.1/bin:/opt/mpich2/gnu/bin/:/storage/vigneshnivas/bin:/home/.your.path.to.sratoolkit.directory./sratoolkit/sratoolkit.2.8.1-ubuntu64/bin:/home/.your.path.to.sratoolkit.directory./sratoolkit/sratoolkit.2.8.1-ubuntu64/bin: No such file or directory

this is problem not convert for the fastq format

[firatuyulur]

hi again, When I said export PATH=$PATH:/home/.your.path.to.sratoolkit.directory./sratoolkit/sratoolkit.2.8.1-ubuntu64/bin, you see the part " /.your.path.to.sratoolkit.directory./ "for my case it is, /home/firat/sratoolkit/sratoolkit.2.8.1-ubuntu64/bin. type it according to your OWN directory. easy way to do this is, go the the folder ../sratoolkit.2.8.1-ubuntu64/bin and right click, press "open in terminal". and in terminal, type "pwd". use that path. I hope this time it will work.

[Michael]

Unfortunately, I don't think this thread makes much sense, at least if one party takes /home/.your.path.to.sratoolkit.directory./ literally.

vigneshnivas09 should get basic training in using linux, we cannot do this on Biostars.

[vigneshnivas09]

i will install this software but not working , no file such or directory sir sir please help me

[Michael]

please drop your sir sir and spend some time reading the docs.

Answer 3

[firatuyulur]

hi, there is a toolkit called sratoolkit. inside of it, there is a subtool called fastq-dump. once you install sratoolkit, go to the bin of sratoolkit folder, type "fastq-dump <accession number="">" and it puts the fastq format of that sra file to your current directory. could you share the source link of that specific sra? I couldnt find such sra in EBI SRA or GEO