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Site Identification from Short Read Sequences.
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Bowtie2 Version #66

Open BobLiterman opened 6 years ago

BobLiterman commented 6 years ago

Hello all,

As @anderspitman found earlier, different versions of Bowite2 give slightly different mapping data. I noticed that in the Docker version is using v.2.3.3.1, while I was using 2.3.4 locally, and 2.2.4 on my cluster.

I think that it would be wise for everyone to use the same Bowtie2 version for testing, and in that vein I recommend that we all (and the Docker) upgrade to the latest major release (v.2.3.4).

I ran a test while 2.3.3.1 and 2.3.4 give identical results, versions < 2.3 do not.

anderspitman commented 6 years ago

Agree. I forgot that this one of the biggest reasons I recommend Docker for development testing. It's the easiest way to ensure a consistent environment

On Mon, Apr 9, 2018, 12:14 PM Bob Literman notifications@github.com wrote:

Hello all,

As @anderspitman https://github.com/anderspitman found earlier, different versions of Bowite2 give slightly different mapping data. I noticed that in the Docker version is using v.2.3.3.1, while I was using 2.3.4 locally, and 2.2.4 on my cluster.

I think that it would be wise for everyone to use the same Bowtie2 version for testing, and in that vein I recommend that we all (and the Docker) upgrade to the latest major release (v.2.3.4).

I ran a test while 2.3.3.1 and 2.3.4 give identical results, versions < 2.3 do not.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/rachelss/SISRS/issues/66, or mute the thread https://github.com/notifications/unsubscribe-auth/AHdTqHwcIt5yEu5hnDoi17MaxpYUlkWnks5tm7MggaJpZM4TNEip .

anderspitman commented 6 years ago

@BobLiterman re updating the Docker image to Bowtie2 version 2.3.4: Based on the changes you've made, and on the fact that I may have generated invalid test data (see #36 discussion), I think we're going to need to redo the test data ASAP and somehow ensure it's valid. That would be a good time to update the Docker image as well.