Question

what do read with blue outline represent in IGV?

0

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7.2 years ago

aindap ▴ 120

Dumb question, but I can't seem to find the answer in the IGV docs. I am unable to upload a screenshot due to restrictions, but I am viewing my alignments of Illumina PE reads aligned with BWA mem. Do the reads with a blue outline indicate improper insert size?

IGV alignment • 4.2k views

ADD COMMENT • link updated 7.2 years ago by Biomonika (Noolean) 3.2k • written 7.2 years ago by aindap ▴ 120

1

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7.2 years ago

agata88 ▴ 870

As far as I know the blue read indicate read from forward strand, red - reverse, grey - both.

Best,

Agata

ADD COMMENT • link 7.2 years ago by agata88 ▴ 870

score 3 · Accepted Answer · 2017-02-01

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7.2 years ago

Biomonika (Noolean) 3.2k

Could this page help?

for an inferred insert size that is smaller than expected (insertion) igv/interpreting_insert_size

ADD COMMENT • link 7.2 years ago by Biomonika (Noolean) 3.2k