Nanopore sequencing BAM file

[Hayden Jones]

Hi,

When I load a BAM file generated from Nanopore reads, there are some areas that have multiple reads on the same line. These reads arent seperated by the usual line that indicated a splice junction. For example,

Read --------Read                      Read ------ Read ------- Read                    Read ------- Read

I know that usually each line would suggest a read and that there are seperated by a spliced line. However some of these reads are as I have described. Do you have any reason why this would be? Thanks in advance,

Hayden

[robin...@gmail.com]

Your assumption is not correct, and really I'm not sure I understand your question.   Why shouldn't there be multiple reads "per line"?

[Hayden Jones]

Hi, 

No other genes in the immediate vicinity show this effect. All protein coding genes have one read per line but for a gene I am interested in, it isnt. Would this be IGV organising the reads to save space? Or is there another reason?

[James Robinson]

I'm still not sure I understand your question, a screenshot might help.  There is no significance to what "line" (I assume you mean row) a read falls on.   If you are seeing a single row of reads somewhere that would indicate a coverage of 1X, which is unusual.   You might want to familiarize yourself with the IGV user guid on alignments:  https://software.broadinstitute.org/software/igv/AlignmentData.