Hello, I was wondering if I could get some advice on using samtools properly.
I'm trying to analyze an output file from a Bowtie2 alignment which is in .sam format. I first converted the .sam file to .bam using the following command: $ samtools view -S -t -b agaA_1_local.sam > agaA_1_local.bam and I got the following return line: [samopen] SAM header is present: 1 sequences. I noticed a .bam file in my directory, so I tried to use the following line: $ samtools tview agaA_1_local.bam agaA.fasta and got the following errors: [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). I'm not sure what I'm doing wrong? Am I missing some steps? Why is my .bam file not an actual BAM file? Any help on this will be greatly appreciated! Thank you, Aakriti Jain ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
