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Old 09-16-2015, 09:29 AM   #1
Junior Member
Location: Chicago, IL

Join Date: Sep 2015
Posts: 1
Default SAM Flags Explained Improved

Hi all,

Someone may have already done this, but I threw together what I think is an improved version of the Broad Explain SAM Flags tool. I find that tool very helpful, but somewhat lacking in UI and visual design.

In case you don't know what I'm talking about:

My take:

The functionality is the exact same, my take just has some UI improvments.

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Old 09-16-2015, 10:00 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Looks nice!

One critique of both your version and the one from the Broad is that some of the wording isn't really correct. For example, "read reverse strand" isn't the meaning of bit 16. This is best demonstrated in something like bisulfite sequencing, where the reverse complement of a read may be what aligns (thus, bit 16 is set), but the read actually aligns to the forward strand (due to the reverse strand having a different sequence). The only change, then, that I would make is to maybe make a window appear with a longer description if someone hovers over something like "read reverse strand". That would allow you to keep the typically correct but not always plain English labels while allowing users a more complete understanding if they need it.
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