Hi, I tried to convert a SAM file from Bowtie2 output to a BAM file, however, it didn't work. [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

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 library(Rsamtools) asBam("../AlignedData/S1_L001_001.SAM", "../AlignedData/S1_L001_001") What did you try? Also, Bowtie2 will be able to output BAM files directly. Martin > [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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793