| Time |
S |
Nick |
Message |
| 06:12 |
|
|
Vein joined #bioperl |
| 07:41 |
|
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Cryonic joined #bioperl |
| 09:14 |
|
faceface |
rbuels: distribution of sizes? |
| 09:16 |
|
faceface |
also, there is nothing significant about SP6 T7 is there? i.e. there are no strand specific restriction sites taken into consideration when cloning a library of this size? |
| 09:16 |
|
* faceface |
assumes not |
| 09:30 |
|
faceface |
max I have == 315788 # LE_HBa0147G09 |
| 09:30 |
|
faceface |
min I have == 19252 # LE_HBa0040H21 |
| 09:30 |
|
faceface |
but those could be errors. |
| 09:32 |
|
faceface |
mean = 137956.75 |
| 09:32 |
|
faceface |
(sample size 20) |
| 12:29 |
|
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kyanardag joined #bioperl |
| 12:35 |
|
faceface |
mc buels! |
| 12:35 |
|
faceface |
http://imagebin.ca/view/vQy_1Vq.html |
| 12:36 |
|
faceface |
http://imagebin.ca/view/JWGfmc.html |
| 12:36 |
|
faceface |
http://imagebin.ca/view/fts3oYmP.html |
| 12:38 |
|
faceface |
I'm not sure, but I gess everything below 5000 is a problem |
| 12:38 |
|
faceface |
possibly 50,000, but I don't know the library |
| 12:39 |
|
* faceface |
wonders how to calculate 'compression statistics' on this scale |
| 14:48 |
|
rbuels |
faceface: these histograms are distances between paired aligned bac ends? |
| 17:02 |
|
faceface |
rbuels: yup |
| 17:02 |
|
faceface |
for all tomato bes libs |
| 17:02 |
|
|
xp_prg joined #bioperl |
| 17:02 |
|
faceface |
and using a crummy alignment settings |
| 17:03 |
|
faceface |
xp_prg: I use BioPerl to handle DNA sequences |
| 17:04 |
|
rbuels |
xp_prg: i mostly use bioperl for handling seqs and processing annotations |
| 17:05 |
|
rbuels |
xp_prg: but it's all a matter of what corner of bioinformatics you're in. |
| 17:06 |
|
xp_prg |
handling dna sequences in what way if you will? |
| 17:07 |
|
rbuels |
xp_prg: i don't do anything particularly complicated with sequences, mostly just reading them in and writing them out in fasta format, feeding them to various analysis tools (like blast, genomethreader, repeatmasker, etc) |
| 17:08 |
|
rbuels |
xp_prg: faceface is probably more of a proper bioinformaticist than me ;-) |
| 17:25 |
|
xp_prg |
tell me more about how you use blash, genomethreader, repeatmasker :> |
| 17:26 |
|
xp_prg |
blash = blast |
| 17:27 |
|
xp_prg |
I am trying to get a high level overview of how people are doing things with bioperl, I am going to teach a class |
| 17:39 |
|
faceface |
rbuels: genomethreader? |
| 17:40 |
|
faceface |
rbuels: is SP6 forward or reverse? (sorry for being lame) |
| 17:40 |
|
faceface |
xp_prg: one use case... get the result of a sequene alignment - read in the alignments with BioPerl (no need to parse it, cus the standard formats have parsers written) |
| 17:41 |
|
faceface |
print out all lenghts of the hits... |
| 17:41 |
|
faceface |
(where identity > some threshold) |
| 17:41 |
|
faceface |
xp_prg: its quite hacky really |
| 17:41 |
|
faceface |
xp_prg: mostly format conversion is my main use of bioperl |
| 17:43 |
|
xp_prg |
I wish I understood more of what you said |
| 17:44 |
|
xp_prg |
but are you answering rbuels uses or your use? |
| 18:13 |
|
rbuels |
faceface: SP6 is reverse. genometheader is pretty much like exonerate. |
| 20:35 |
|
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veinous joined #bioperl |
| 22:04 |
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kyanardag joined #bioperl |
