Select a list of reads in IGV
1
0
Entering edit mode
2.6 years ago
onca ▴ 10

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,

IGV rna-seq • 1.5k views
ADD COMMENT
1
Entering edit mode
2.6 years ago

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
ADD COMMENT
0
Entering edit mode

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!

ADD REPLY
0
Entering edit mode

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_colored

DT tag in bam file (only for duplicates):

dt_tag_bam

ADD REPLY

Login before adding your answer.

Traffic: 1222 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6