Hi,
I have sequence-information generated on a illumina sequencer. The aligment was done with ELAND and the output is a .bam file.
Now I wanted to generate a pileup-file with the mpileup feature from samtools. I used this command to perform that:
samtools mpileup -f REFERENCEFILE.fa SEUQENCES.bam > pileup.tab
The Problem is that I don't get a reference base, but only N where I expect A,T,G or G.
I also used the sort command before.
Maybe something with the faidx was wrong, because I only have 1 Lane in the .fai file.
Does someone has an answer for that.
Thanks a lot.
I have sequence-information generated on a illumina sequencer. The aligment was done with ELAND and the output is a .bam file.
Now I wanted to generate a pileup-file with the mpileup feature from samtools. I used this command to perform that:
samtools mpileup -f REFERENCEFILE.fa SEUQENCES.bam > pileup.tab
The Problem is that I don't get a reference base, but only N where I expect A,T,G or G.
I also used the sort command before.
Maybe something with the faidx was wrong, because I only have 1 Lane in the .fai file.
Does someone has an answer for that.
Thanks a lot.
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