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