Red arrows

[Konstantinos Gidiotis]

Hi,

So I have two questions regarding IGV.

1) can IGV load/visualize the unplaced reads (*) ?. Since my genome has many uncharacterized regiosn (NNNs) and I would like to see if with the long-reads can cover these areas.

2) I think this is probably related to the first question, so from the picture below I have some reads that are white (I assume quality of 0) but I also have some red arrows at the end of the gray reads. What does this mean? Is this mean that this read continues theoretically further on, but due to uncharacterized regions the read stops?

Please let me know if you have any answer to this. Thanks a lot.

Best,

Kostas

[igv-help]

Hi, answer to (1) is no.   See here https://igv.org/doc/desktop/#UserGuide/tracks/alignments/viewing_alignments_basics/ and here  https://igv.org/doc/desktop/#UserGuide/tracks/alignments/chimeric_reads/#clipping-indicator for answer to other questions.  In brief the red indicates the alignment is clipped.   

[Konstantinos Gidiotis]

Thanks for your reply in this.

The second link cannot be opened though. Is it possible to resend it?

Thanks.

[igv-help]

Sorry about that. See this page https://igv.org/doc/desktop/#UserGuide/tracks/alignments/chimeric_reads/