Bowtie2 Sam output

[Derek-C]

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!

[swbarnes2]

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 a NCBI library 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!

For completeness sake, reads that failed to map are usually included in .bam files. So that's normal. 30% mapping is kind of low. You are aligning to a reference file of transcripts, right? Not genome?

[Derek-C]

For completeness sake, reads that failed to map are usually included in .bam files. So that's normal. 30% mapping is kind of low. You are aligning to a reference file of transcripts, right? Not genome?

Yup thats right.

I'm sorry I'm not quite understanding what you mean? If reads that fail to map are included in another file, then how is it that only 30% of the reads in the other file mapped?

[rflrob]

I think swbarnes was saying that reads that fail to map are included in the same SAM file as the ones that do map. There are options for bowtie that let you put them into a separate file; what does your command string look like?