[BioC] samtools error

Martin Morgan mtmorgan at fhcrc.org
Thu May 31 06:14:46 CEST 2012

On 05/30/2012 08:57 PM, Yu Chuan Tai wrote:
> Hi,
> I tried to convert a SAM file from Bowtie2 output to a BAM file,
> however, it didn't work.

I guess you're talking about Rsamtools; if you mean samtools, then this 
is not the right forum. How did you try to convert the file? It should be

   asBam("../AlignedData/S1_L001_001.SAM", "../AlignedData/S1_L001_001")

What did you try? Also, Bowtie2 will be able to output BAM files directly.


> [bam_header_read] EOF marker is absent. The input is probably truncated.
> [bam_header_read] invalid BAM binary header (this is not a BAM file).
> [main_samview] fail to read the header from
> "../AlignedData/S1_L001_001.SAM".
> When I used Bowtie2, I tried to include SAM headers and not include SAM
> headers, both gave me the same error.
> Could anyone tell me what's going on here, since I just started to use
> samtools today.
> Thanks!
> Yu Chuan
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