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A lot of SRA data is actually stored in bams. This can be downloaded with the sea toolkit as well, but needs to use
sam-dump
instead.
The complete command would look sth like this:
prefetch -v $i sam-dump $i | samtools view -bS - > $i.bam;
The samtools step directly converts the sam to bam for efficiency reasons. $i is the respective accession number
$i
The text was updated successfully, but these errors were encountered:
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A lot of SRA data is actually stored in bams. This can be downloaded with the sea toolkit as well, but needs to use
instead.
The complete command would look sth like this:
The samtools step directly converts the sam to bam for efficiency reasons.
$iis the respective accession numberThe text was updated successfully, but these errors were encountered: