[BioC] samtools error
mtmorgan at fhcrc.org
Thu May 31 06:14:46 CEST 2012
On 05/30/2012 08:57 PM, Yu Chuan Tai wrote:
> 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
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
> 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.
> Yu Chuan
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