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bailey-lab / SeekDeep

Bioinformatic Tools for analyzing targeted amplicon sequencing developed by Nicholas Hathaway of Bailey Lab
http://seekdeep.brown.edu/
GNU Lesser General Public License v3.0
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--processed #9

Closed nikosdarzentas closed 4 years ago

nikosdarzentas commented 4 years ago

Hello Nick, I've been trying SeekDeep the last few days to see if it can help us in our antigen receptor sequence analysis, since it has some potentially very useful features. But I have some questions / issues, which I'll lay down separately.

First question is how this works, i.e. what's the suffix? An example would be great.

--processed Processed, Input Sequence Name has a suffix that contains abundance info

Many thanks in advance, I'll be back with more :-)

nickjhathaway commented 4 years ago

So the suffix can be HapSeq.01_[NUMBER] or HapSeq.01_t[NUMBER] where NUMBER is the abundance information e.g.

HapSeq.01_10 or HapSeq.01_t10

These above would say there are 10 of these sequences rather than just 1.

Let me know if that helps.

Nick

nikosdarzentas commented 4 years ago

Ah yes, I've seen "_t10" in the output - thank you.