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Counting sense and anti-sense reads

asked 2016-10-25 13:55:16 -0600

Ammar Husami gravatar image

When I double click on a position, the following statistics shows

Chr2: 230,329,571 Matches / Mismatches / Deletions Type Base Count % of Total Mean Quality (match) A 59 75.6 27.5 (mismatch) T 1 1.3 18.0 (deletion) 18 23.1 ? Total 78 100 27.4

0 alignments filtered out by quality settings.

Chr2 between 230,329,570 and 230,329,571 Insertions Base(s) Count % of Total Mean Quality Non-Insertions 78 100.0 ? Total 78 100 ?

Note: Any alignment spanning or adjacent to the insertion junction that does not have an insertion at the junction is counted as a non-insertion.

is there way to count which reads are on the sense and anti-sense strands?

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answered 2016-11-01 10:00:45 -0600

Hey Ammar,

Our summary table here does not break out forward/reverse strand counts. Our default coloring scheme is based on forward/reverse mappings and there is also in the gear menu of the Pile-Up plot an option to "Split by Strand', which gives you a very nice visualization of strand-bias by placing all forward reads above and reverse reads below the axis.

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Example stacking:

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Asked: 2016-10-25 13:55:16 -0600

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Last updated: Nov 01 '16