SEA-PHAGES | All posts created by edgingtonn1

Link to this post \| posted 10 Apr, 2017 14:32
edgingtonn1	Hi, It seems that the Z-scores from PECAAN differ from the Z-scores from DNAMaster for a given gene, and for the same start sites. Any idea why? Both scores for the same gene start always seem to show the same trend, so it doesn't seem like a big issue– just a curiosity for now. Which one should be in the final annotation notes? We are going with the PECAAN ones since they are all imported into DNAMaster at once. Best, -Nick SCSU, New Haven CT

Link to this post | posted 10 Apr, 2017 14:32

Hi,

It seems that the Z-scores from PECAAN differ from the Z-scores from DNAMaster for a given gene, and for the same start sites. Any idea why? Both scores for the same gene start always seem to show the same trend, so it doesn't seem like a big issue– just a curiosity for now. Which one should be in the final annotation notes? We are going with the PECAAN ones since they are all imported into DNAMaster at once.

Best,
-Nick
SCSU, New Haven CT

Posted in: PECAAN → PECAAN Z-scores differ from DNAMasters

Link to this post \| posted 22 Feb, 2017 17:26
edgingtonn1	Thanks Chris – Yup, that was the issue! I'm not sure how it ended up locked, but it was indeed locked. Cheers, -Nick

Posted in: PECAAN → Read-only Genome for User?

Link to this post \| posted 22 Feb, 2017 16:29
edgingtonn1	My students are having a problem editing the Mabel genome in PECAAN, with the error stating that it is “Read-only", and thus cannot be edited/annotated. The same students can edit other SCSU genomes that have been added, but not Mabel. As an Admin, I have no problems editing Mabel. Any idea why there is a permissions error even thought they are approved Institutional Users? Best, -Nick Edited 22 Feb, 2017 16:31

Link to this post | posted 22 Feb, 2017 16:29

edgingtonn1

My students are having a problem editing the Mabel genome in PECAAN, with the error stating that it is “Read-only", and thus cannot be edited/annotated. The same students can edit other SCSU genomes that have been added, but not Mabel. As an Admin, I have no problems editing Mabel. Any idea why there is a permissions error even thought they are approved Institutional Users?

Best,
-Nick

Edited 22 Feb, 2017 16:31

Posted in: PECAAN → Read-only Genome for User?

Link to this post \| posted 08 Feb, 2017 18:20
edgingtonn1	Hi Chris, We were attempting to perform the whole phamerated phage report for Flaverint, and it crashed on gp18. It seems to happen with the 2017VM Starterator, and the Github V1.1 version that I 'git cloned'. In fact, Starterator doesn't seem to like many of the A11's. Best, -Nick

Posted in: Starterator → phage that crash starterator

Link to this post \| posted 06 Feb, 2017 22:20
edgingtonn1	Flaverint_Draft (A11) crashes at Gene 18 (Pham 8250) with the code below using the Starterator 1.1 from github. (I can however, get the Pham report from the WUSTL website.) Thanks, -Nick CLUSTAL 2.1 Multiple Sequence Alignments Sequence format is Pearson Sequence 1: Jabith_Draft_31 204 bp Sequence 2: Lucivia_Draft_32 204 bp Sequence 3: Flaverint_Draft_31 204 bp Sequence 4: Bachome_Draft_31 204 bp Start of Pairwise alignments Aligning… Sequences (1:2) Aligned. Score: 100 Sequences (1:3) Aligned. Score: 100 Sequences (1:4) Aligned. Score: 98.0392 Sequences (2:3) Aligned. Score: 100 Sequences (2:4) Aligned. Score: 98.0392 Sequences (3:4) Aligned. Score: 98.0392 Guide tree file created: [/home/seafaculty/.starterator/Intermediate Files/Pham8250.dnd] There are 3 groups Start of Multiple Alignment Aligning… Group 1: Sequences: 2 Score:3876 Group 2: Sequences: 3 Score:3876 Group 3: Sequences: 4 Score:3838 Alignment Score 9738 CLUSTAL-Alignment file created [/home/seafaculty/.starterator/Intermediate Files/Pham8250.aln] exception in starterator Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner self.run() File "/home/seafaculty/starterator/starterator/uiStarterate.py", line 296, in run self.starterate() #running thread starts here File "/home/seafaculty/starterator/starterator/uiStarterate.py", line 301, in starterate gui=self, event=self.stop_thread) File "/home/seafaculty/starterator/starterator/starterate.py", line 112, in starterate final_file, short_final = phage.final_report() File "/home/seafaculty/starterator/starterator/report.py", line 59, in final_report self.make_reports() File "/home/seafaculty/starterator/starterator/report.py", line 84, in make_reports pham = gene_report.make_report(whole=True) File "/home/seafaculty/starterator/starterator/report.py", line 283, in make_report self.pham.find_most_common_start() File "/home/seafaculty/starterator/starterator/phams.py", line 233, in find_most_common_start most_annot_start_index = self.total_possible_starts.index(annot_starts_count[0][0])+1 IndexError: list index out of range

Link to this post | posted 06 Feb, 2017 22:20

edgingtonn1

Flaverint_Draft (A11) crashes at Gene 18 (Pham 8250) with the code below using the Starterator 1.1 from github. (I can however, get the Pham report from the WUSTL website.)

Thanks,
-Nick

CLUSTAL 2.1 Multiple Sequence Alignments

Sequence format is Pearson
Sequence 1: Jabith_Draft_31      204 bp
Sequence 2: Lucivia_Draft_32     204 bp
Sequence 3: Flaverint_Draft_31   204 bp
Sequence 4: Bachome_Draft_31     204 bp
Start of Pairwise alignments
Aligning…

Sequences (1:2) Aligned. Score: 100
Sequences (1:3) Aligned. Score: 100
Sequences (1:4) Aligned. Score: 98.0392
Sequences (2:3) Aligned. Score: 100
Sequences (2:4) Aligned. Score: 98.0392
Sequences (3:4) Aligned. Score: 98.0392
Guide tree file created:   [/home/seafaculty/.starterator/Intermediate Files/Pham8250.dnd]

There are 3 groups
Start of Multiple Alignment

Aligning…
Group 1: Sequences:   2      Score:3876
Group 2: Sequences:   3      Score:3876
Group 3: Sequences:   4      Score:3838
Alignment Score 9738

CLUSTAL-Alignment file created  [/home/seafaculty/.starterator/Intermediate Files/Pham8250.aln]

exception in starterator
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
  File "/home/seafaculty/starterator/starterator/uiStarterate.py", line 296, in run
    self.starterate() #running thread starts here
  File "/home/seafaculty/starterator/starterator/uiStarterate.py", line 301, in starterate
    gui=self, event=self.stop_thread)
  File "/home/seafaculty/starterator/starterator/starterate.py", line 112, in starterate
    final_file, short_final = phage.final_report()
  File "/home/seafaculty/starterator/starterator/report.py", line 59, in final_report
    self.make_reports()
  File "/home/seafaculty/starterator/starterator/report.py", line 84, in make_reports
    pham = gene_report.make_report(whole=True)
  File "/home/seafaculty/starterator/starterator/report.py", line 283, in make_report
    self.pham.find_most_common_start()
  File "/home/seafaculty/starterator/starterator/phams.py", line 233, in find_most_common_start
    most_annot_start_index = self.total_possible_starts.index(annot_starts_count[0][0])+1
IndexError: list index out of range

Posted in: Starterator → phage that crash starterator

Link to this post \| posted 22 Jan, 2017 15:41
edgingtonn1	Is the http://cobamide2.bio.pitt.edu/ server down (between Jan. 21nd-22nd, 2017)? The ftp server is not responding. I have tried CLI, several browsers and two operating systems to connect, and they all have failed. If it is not an error on my side, it would be nice if a message was posted somewhere (or an email to SEA-PHAGES faculty) that the server is down for regular maintenance, etc.

Posted in: DNA Master → Can't get DNA Master to download on a PC

Link to this post \| posted 15 Dec, 2016 16:22
edgingtonn1	Awesome! Thanks Chris!

Posted in: Starterator → Starterator version 1.1 released

Link to this post \| posted 17 Nov, 2016 15:21
edgingtonn1	My students are having a very tough time getting a high enough yields with this new protocol! We may not make the deadline of tomorrow (11-18-16). We are following the protocol and keeping in mind all of the potential pitfalls with the kit. We have seen a little smearing on the "best" preps, and we have one prep that also does the disappearing trick after R.E. digestion. With the caveats of a NanoDrop in mind, we are getting ~40ng/uL to ~80ng/uL following the protocol, and in several cases when we did not split the one mL HTL (i.e. added 1mL of HTL to one column), the resulting yield was double (i.e. ~160ng/uL), which might be useful to know. Our lysate titers have been low as well, thus we have been working with lysates very close to 1x10^9 pfu/mL, because it has been the best that the students have been able to achieve this year (which is a separate issue to be sure.) Dan: With such great sequence coverage that has been seen from past years, would the contaminating host DNA really cause much of a problem with assembly? Maybe one could just add a bit of RNAse directly to the HTL's? It would be interesting to know if you have ever tried phage genomic sequencing with and without the addition of the DNAse/RNAse cocktail, and compared the assembly results.

Link to this post | posted 17 Nov, 2016 15:21

edgingtonn1

My students are having a very tough time getting a high enough yields with this new protocol! We may not make the deadline of tomorrow (11-18-16). We are following the protocol and keeping in mind all of the potential pitfalls with the kit. We have seen a little smearing on the "best" preps, and we have one prep that also does the disappearing trick after R.E. digestion. With the caveats of a NanoDrop in mind, we are getting ~40ng/uL to ~80ng/uL following the protocol, and in several cases when we did not split the one mL HTL (i.e. added 1mL of HTL to one column), the resulting yield was double (i.e. ~160ng/uL), which might be useful to know. Our lysate titers have been low as well, thus we have been working with lysates very close to 1x10^9 pfu/mL, because it has been the best that the students have been able to achieve this year (which is a separate issue to be sure.)

Dan: With such great sequence coverage that has been seen from past years, would the contaminating host DNA really cause much of a problem with assembly? Maybe one could just add a bit of RNAse directly to the HTL's? It would be interesting to know if you have ever tried phage genomic sequencing with and without the addition of the DNAse/RNAse cocktail, and compared the assembly results.

Posted in: Phage Discovery/Isolation → Yield and degradation of DNA isolated by new protocol

Link to this post \| posted 15 Dec, 2015 15:14
edgingtonn1	Hello Anthony, This file has the instructions for the manual installation of Phamerator. We have done this before, and it worked fine. Best, -Nick

Posted in: SEA-PHAGES Virtual Machine → Individual software components for Ubuntu users

Link to this post \| posted 23 Nov, 2015 16:26
edgingtonn1	The "pham circle" tool is broken in Phamerator, and I believe that Steve C. is aware of this. In the meanwhile, if you can do some programming, Circos is an option to draw something similar.

Posted in: Phamerator → Phams

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