Question: How to convert a batch of .sra NGS files to BAM,SAM, fasta formats?
0
gravatar for vassialk
2.7 years ago by
vassialk150
Belarus
vassialk150 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 • 2.2k views
ADD COMMENTlink modified 2.7 years ago by Antonio R. Franco3.5k • written 2.7 years ago by vassialk150
2
gravatar for Antonio R. Franco
2.7 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco3.5k 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 COMMENTlink written 2.7 years ago by Antonio R. Franco3.5k

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

ADD REPLYlink written 2.7 years ago by apelin20460

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

ADD REPLYlink written 2.7 years ago by vassialk150

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 REPLYlink written 2.7 years ago by apelin20460

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

ADD REPLYlink written 2.7 years ago by vassialk150
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