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Question: How to generate .sra files from Fastq
2
gravatar for ktsuttlemyre
4.4 years ago by
ktsuttlemyre • 40
United States
ktsuttlemyre • 40 wrote:

I have been downloading a lot of NCBI short read archive files (.sra files) and I know how to convert them to bam, sam, fastq, etc but is there a way to generate my own .sra files? The tools in the SRA toolkit do not seem to convert to .sra

 

​Relevant Information:

SRA toolkit
http://eutils.ncbi.nih.gov/Traces/sra/?view=software
Handbook
http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.5_Converting_SRA_for
file format sequence fastq sra ncbi • 3.5k views
ADD COMMENT • link •
modified 4.4 years ago by Devon Ryan ♦ 85k • written 4.4 years ago by ktsuttlemyre • 40

Out of curiosity: what would you like to do with *.sra files when you already have the *.bam/*.sam/*.fastq files?

ADD REPLY • link written 4.2 years ago by polarise • 370
3
gravatar for Pawel Szczesny
4.4 years ago by
Pawel Szczesny ♦ 3.2k
Poland
Pawel Szczesny ♦ 3.2k wrote:

I have never used it but Mothur has a command "make.sra".
ADD COMMENT • link written 4.4 years ago by Pawel Szczesny ♦ 3.2k
2
gravatar for Devon Ryan
4.4 years ago by
Devon Ryan ♦ 85k
Freiburg, Germany
Devon Ryan ♦ 85k wrote:

You would use one of the X-load tools from the SRA toolkit, where X is bam, fastq, etc. Now why you would actually want to do this is beyond me. You're better off sticking to BAM and fastq, which are actually normal formats used by tools.
ADD COMMENT • link written 4.4 years ago by Devon Ryan ♦ 85k
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