Select a list of reads in IGV

Question

[onca]

Hi everyone,

Is there anyway of selecting a list of reads in IGV? I would like to highlight a group of reads based on their ids or coordinates. I have duplicates on my RNA-Seq that I would like to visualize in IGV.

Thanks,

Answer 1

[Pierre Lindenbaum]

you can add a YC tag in the reads you want:

https://software.broadinstitute.org/software/igv/ReleaseNotes/2.4.x

1. Alignment coloring. Coloring by “YC” tag can now be explicitly enabled and disabled through the “Color By” option of the alignment track pop-up menu. The menu item “Color By YC Tag” will appear, selected by default, if YC tags are used

[onca]

Hi,

In fact, I have already run Picard MarkDuplicates which indicates the duplicates through sam/bam flag field. But it can also add a duplicate type (DT) tag:

Although the bitwise flag annotation indicates whether a read was marked as a duplicate, it does not identify the type of duplicate. To do this, a new tag called the duplicate type (DT) tag was recently added as an optional output in the 'optional field' section of a SAM/BAM file. Invoking the TAGGING_POLICY option, you can instruct the program to mark all the duplicates (All), only the optical duplicates (OpticalOnly), or no duplicates (DontTag). The records within the output of a SAM/BAM file will have values for the 'DT' tag (depending on the invoked TAGGING_POLICY), as either library/PCR-generated duplicates (LB), or sequencing-platform artifact duplicates (SQ).

Do you think if I re-run Picard MarkDuplicates with this option I will be able to highlight the duplicates in IGV (through "Color alignments by > tag > DT")?

Thanks!

[onca]

Just an update: I was indeed able to visualize the duplicates in IGV by "Color alignments by > tag > DT".

IGV image with duplicates highlighted in red:

DT tag in bam file (only for duplicates):