Hi everyone

Can you please help me to extract SAM file from SRA?

I took the dataset from here http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1208162

Downloaded SRA file.

Then did sra-dump on this (as it is said on the page of dataset that reads are already aligned).

But as a result I got very small file (~50 Mb). When I tried to convert it to sorted BAM file I got:

```
[bam_header_read] EOF marker is absent. The input is probably truncated.
[sam_header_line_parse] expected '@XY', got [@HD VN:1.3]
Hint: The header tags must be tab-separated.
[samopen] no @SQ lines in the header.
```

I tried to look at summary information of this SRA file here: http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR951914

And didn't see any information about alignment

Tried to look at alignment information by command:

    vdb-dump ./SRR951915.sra | grep "ALIGNMENT_COUNT"

got an error

```
vdb-dump.2.1.7 int: data bad version while constructing page map within virtual database module - VCursorCellData( col:PANEL at row #1074 ) failed
fastq-dump command led to an error: data bad version while constructing page map within virtual database module - failed SRR951914.sra
```

Any idea?
Hi, yesterday I got a good output from fastq-dump.

Your command line is wrong. To run fastq-dump correctly you should know whether your reads are single or paired. In your case, we have single reads, then the command line will be:

    ./fastq-dump --split-spot SRR951914.sra

For paired reads:

    ./fastq-dump --split-files *file*.sra