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Question: How to convert a batch of .sra NGS files to BAM,SAM, fasta formats?
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gravatar for vassialk
3.7 years ago by
vassialk • 190
Belarus
vassialk • 190 wrote:

How to convert a batch of .sra NGS files to BAM, SAM, fasta formats? I found SRA toolkit, is there a better solution?
sam bam ngs sra • 2.6k views
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modified 3.7 years ago by Antonio R. Franco • 3.9k • written 3.7 years ago by vassialk • 190
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gravatar for Antonio R. Franco
3.7 years ago by
Antonio R. Franco • 3.9k
Spain. Universidad de Córdoba
Antonio R. Franco • 3.9k wrote:

If working with linux you can use parallel

sudo apt-get install parallel

after installing parallel, you can convert all of your SRA to either FastQ or Fasta files, but not to BAM/SAM because these files contains information about mapping that is not contained into your SRA files

$find *.sra | parallel 'fastq-dump {}' # To get the FastQ files

$find *.sra | parallel 'fastq-dump -- fasta {}'   # To get the Fasta files
ADD COMMENT • link written 3.7 years ago by Antonio R. Franco • 3.9k

Or if you want to convert them sequentially for i in *.sra; do fastq-dump $i; done

ADD REPLY • link written 3.7 years ago by apelin20 • 470

Thank you, I`ll try. Is there any desktop application for that?

ADD REPLY • link written 3.7 years ago by vassialk • 190

Unfortunatly there is no better solution than the SRA toolkit, which is the only one so far that I know of that can handle SRA data. The commands suggested here require a unix based platform.

ADD REPLY • link written 3.7 years ago by apelin20 • 470

How to run sra toolkit to convert a batch of files in the directory?

ADD REPLY • link written 3.7 years ago by vassialk • 190
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