Question: How to split a merge piared data using ncbi SRA tools?
0
gravatar for souradeep.galaxy
13 months ago by
souradeep.galaxy10 wrote:

can I split a merged paired end extract reads into two separate data (acc. to their ends) using ncbi SRA tools?

fastq qa paired ncbi sra tools • 537 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by souradeep.galaxy10
1
gravatar for Guy Reeves
13 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

Hi Personally, I avoid having to split SRA data by using the EBI site which mirrors the same SRA data as NCBI but also given the option of already split files (the ID numbers are the same on both). Also by using the 'getdata>EBI SRA' tool which It think is on all galaxy instances you also have the option to download directly into galaxy. However using the tool 'fastq_paired_end_splitter' should give the same result. Cheers Guy

ADD COMMENTlink written 13 months ago by Guy Reeves1.0k
0
gravatar for souradeep.galaxy
13 months ago by
souradeep.galaxy10 wrote:

I know that Guy, the problem i am facing during uploading the data to galaxy main directly through EBI, is that the files which gets uploaded are of .gz format, and i am unable to extract it. Due to which i am unable to process the data any further. Yeah, another problem about the fastq paired end splitter is that it's not working upon my data as it is too large.

ADD COMMENTlink written 13 months ago by souradeep.galaxy10

1Are you on usegalaxy.org? 2are you using the tool 'getdata>EBI SRA' 3 what happens to the downloaded dataset ( grey , yellow , green, red?). does it have an extension in its name?

Galaxy should automatically deal with .gz files without you noticing. I will try to help once I have answers to the above.

ADD REPLYlink written 13 months ago by Guy Reeves1.0k

1 Yes i am on usegalaxy 2 yes i am using getdata>EBI_SRA 3 the dataset is green 4 the extension is coming as fastq.gz. and yup automatically galaxy used to unzip all the files but right now it's not happening.

Anyway Guy thank you for staying in touch..Thank you soo much. :) anyway what i m doing is now that i am downloading the .gz file from ebi and then using groomer changing its format. I hope this will work.

ADD REPLYlink written 13 months ago by souradeep.galaxy10

Do you have any better idea...please share...Thanks..

ADD REPLYlink written 13 months ago by souradeep.galaxy10
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