Question: sam-dump output is empty
gravatar for 592081962
3.5 years ago by
59208196210 wrote:

Hi, everyone. I download a SRA dataset (SRR645175) from SRA database. Now I want convert it to BAM format. As far as I know I should use sam-dump to convert it to SAM format than to BAM with samtools. Here is the problem. When I execute sam-dump SRR645175 it takes only seconds and generates nothing. Then I tried sam-dump SRR645175 --output-file SRR645175.sam. The output is an empty file. Can someone help me to solve this problem? Also If the issue is inevitable is it OK to take a roundabout like converting the SRA data to Fasta then to BAM?

sequencing software error • 1.8k views
ADD COMMENTlink written 3.5 years ago by 59208196210

From what I can see, the BioProject associated with this Run identifier does not provide the mapped reads. You should be using fastq-dump to get the reads, and then do the mapping yourself. Unless of course you wanted the raw unmapped reads in sam format?

ADD REPLYlink written 3.5 years ago by James Ashmore3.0k

You are right. The raw data was unaligned. If I use sam-dump with a -u option which gives unaligned sequence as well I can get full output.

ADD REPLYlink written 3.5 years ago by 59208196210
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