Hey guys,
I'm somewhat new to bioinformatics and I'm using bowtie2 with transcriptomic data, but there's something I don't quite understand. I'm mapping my transcripts to a version of the NCBI database in order to try to identify them. When I put the output sam file from bowtie2 into samtools and run flagstats on them it says (among other things)
Y + 0 mapped (x%:nan%)
That percentage has been somewhat low (~ 30 %)
But I thought the sam output file contained all the reads that were mapped against the reference database? How can only a certain percentage of this sam file contain mapped reads? Or am I misunderstanding something here? Thanks in advance!
I'm somewhat new to bioinformatics and I'm using bowtie2 with transcriptomic data, but there's something I don't quite understand. I'm mapping my transcripts to a version of the NCBI database in order to try to identify them. When I put the output sam file from bowtie2 into samtools and run flagstats on them it says (among other things)
Y + 0 mapped (x%:nan%)
That percentage has been somewhat low (~ 30 %)
But I thought the sam output file contained all the reads that were mapped against the reference database? How can only a certain percentage of this sam file contain mapped reads? Or am I misunderstanding something here? Thanks in advance!
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