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biocore / deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.
BSD 3-Clause "New" or "Revised" License
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support for other amplicon types #122

Closed cuttlefishh closed 7 years ago

cuttlefishh commented 7 years ago

Does Deblur work with amplicon types other than 16S? I have tried running it on ITS and 18S but I'm not sure it's working properly.

mortonjt commented 7 years ago

Yup - it works on other amplicon data types. But you do need to turn off positive mode - since that will only keep the reads that hits greengenes.

rob-knight commented 7 years ago

is positive mode tied specifically to greengenes or can you pick the ref db? (I hope the latter)

On Dec 7, 2016, at 12:30 PM, Jamie Morton notifications@github.com<mailto:notifications@github.com> wrote:

Yup - it works on other amplicon data types. But you do need to turn off positive mode - since that will only keep the reads that hits greengenes.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/biocore/deblur/issues/122#issuecomment-265564313, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AB69KbjWEPgZ1skLSIveXO2E8m8hmfVXks5rFxdXgaJpZM4LG6vb.

wasade commented 7 years ago

User controllable, just needs fasta, but defaults and ships with greengenes 88%

On Dec 7, 2016 12:37 PM, "Rob Knight" notifications@github.com wrote:

is positive mode tied specifically to greengenes or can you pick the ref db? (I hope the latter)

On Dec 7, 2016, at 12:30 PM, Jamie Morton <notifications@github.com<mailto: notifications@github.com>> wrote:

Yup - it works on other amplicon data types. But you do need to turn off positive mode - since that will only keep the reads that hits greengenes.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ biocore/deblur/issues/122#issuecomment-265564313, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AB69KbjWEPgZ1skLSIveXO2E8m8hmfVXks5rFxdXgaJpZM4LG6vb>.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore/deblur/issues/122#issuecomment-265566199, or mute the thread https://github.com/notifications/unsubscribe-auth/AAc8sjkJoHBktziOGj7V5afhWjbdSK-Mks5rFxkmgaJpZM4LG6vb .

rob-knight commented 7 years ago

thanks for clarification!

On Dec 7, 2016, at 12:40 PM, Daniel McDonald notifications@github.com<mailto:notifications@github.com> wrote:

User controllable, just needs fasta, but defaults and ships with greengenes 88%

On Dec 7, 2016 12:37 PM, "Rob Knight" notifications@github.com<mailto:notifications@github.com> wrote:

is positive mode tied specifically to greengenes or can you pick the ref db? (I hope the latter)

On Dec 7, 2016, at 12:30 PM, Jamie Morton notifications@github.com<mailto:notifications@github.com<mailto: notifications@github.commailto:notifications@github.com>> wrote:

Yup - it works on other amplicon data types. But you do need to turn off positive mode - since that will only keep the reads that hits greengenes.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ biocore/deblur/issues/122#issuecomment-265564313, or mute the thread< https://github.com/notifications/unsubscribe-auth/ AB69KbjWEPgZ1skLSIveXO2E8m8hmfVXks5rFxdXgaJpZM4LG6vb>.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore/deblur/issues/122#issuecomment-265566199, or mute the thread https://github.com/notifications/unsubscribe-auth/AAc8sjkJoHBktziOGj7V5afhWjbdSK-Mks5rFxkmgaJpZM4LG6vb .

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/biocore/deblur/issues/122#issuecomment-265566877, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AB69KXs4J0DhFo-UH0-ppgivlptjNtuDks5rFxm9gaJpZM4LG6vb.

cuttlefishh commented 7 years ago

Thanks all. Would be helpful to specify this in the documentation and --help message.

wasade commented 7 years ago

@cuttlefishh can you review the current content of the README in master and close this issue if appropriate?