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Search: Posts Made By: WaltL
Forum: Bioinformatics 05-08-2013, 07:40 AM
Replies: 9
Views: 11,877
Posted By WaltL
I use FastQC all the time. Very nice tool;...

I use FastQC all the time. Very nice tool; however, unless I'm missing something, it neither gives the mean read length (it does give the size range and a graphical distribution of read length) nor...
Forum: Bioinformatics 01-08-2013, 12:05 PM
Replies: 2
Views: 5,436
Posted By WaltL
Mean insert = 4400 b Still a draft- 1386...

Mean insert = 4400 b


Still a draft- 1386 scaffolds



Based on common assembly metrics, some are better some are worse. For example, scaffold metrics:

####scaffs, total_size, ...
Forum: Bioinformatics 01-06-2013, 06:29 AM
Replies: 2
Views: 5,436
Posted By WaltL
Best approach- genome de novo assembly with reference

I have some new Illumina data (HiSeq 100b reads- one paired-end (94xe6 reads) and one mate-pair (54xe6 reads) lib.) for a fungal genome (ca. 30MB) for which a pretty good reference is already...
Forum: Bioinformatics 09-10-2012, 12:05 PM
Replies: 4
Views: 3,418
Posted By WaltL
I'm trying some different tools out to see which...

I'm trying some different tools out to see which works best. I've used FastQC to identify problems and adapter seqs in the reads. Next, I used cutadapter to trim, and now I'm trying the fastq qual...
Forum: Bioinformatics 09-10-2012, 09:35 AM
Replies: 4
Views: 3,418
Posted By WaltL
Ahhhhh, thank you... that worked!

Ahhhhh, thank you... that worked!
Forum: Bioinformatics 09-10-2012, 09:07 AM
Replies: 4
Views: 3,418
Posted By WaltL
FastX-Toolkit qual_filter error

I'm trying to us FastX Toolkit for the first time- running the quality filter on an Illumina sr dataset (1.9 encoding) as follows:

fastq_quality_filter -v -q 30 -p 88 -i input_name.fq -o...
Forum: 454 Pyrosequencing 01-20-2011, 01:56 PM
Replies: 30
Views: 22,495
Posted By WaltL
Installation of Newbler version 2.5.3 on Ubuntu...

Installation of Newbler version 2.5.3 on Ubuntu 10.04.1 (Lucid Lynx) without using the supplied Nixstaller.

Important Note: Do not cut and paste the commands below. Type them in.

Important...
Forum: 454 Pyrosequencing 01-19-2011, 05:25 AM
Replies: 30
Views: 22,495
Posted By WaltL
I worked on it most of the day and finally got it...

I worked on it most of the day and finally got it installed. :D

It is not too difficult, but you cannot use the installer. I am performing a test assembly this morning and I will post...
Forum: 454 Pyrosequencing 01-18-2011, 12:00 PM
Replies: 30
Views: 22,495
Posted By WaltL
Installing Newbler 2.5.3 on 64 bit Ubuntu...anyone???

Just wondering if anyone has managed a successful install of Newbler 2.5.3 on later versions of Ubuntu.

I have the previous version installed and working fine on Ubuntu 10.04. However, the latest...
Forum: 454 Pyrosequencing 12-08-2010, 05:38 PM
Replies: 2
Views: 1,943
Posted By WaltL
Lex, Thanks for your response. So I went...

Lex,

Thanks for your response. So I went back and double checked and you are correct, there are contigs in the 454Isotig.fna file. I greped contig and found 1,113 instances... the difference of...
Forum: 454 Pyrosequencing 12-03-2010, 01:21 PM
Replies: 4
Views: 2,263
Posted By WaltL
There is a SOLiD forum here: ...

There is a SOLiD forum here:

http://seqanswers.com/forums/forumdisplay.php?f=7
Forum: 454 Pyrosequencing 12-03-2010, 12:35 PM
Replies: 2
Views: 1,943
Posted By WaltL
Question Why does Newbler do what it does with .ace files?

First, let me say that I've contacted Roche tech support multiple times and still have not received an answer. If I could talk to a Newbler programmer, perhaps they would shed some light, but you'll...
Forum: 454 Pyrosequencing 12-03-2010, 11:28 AM
Replies: 4
Views: 2,263
Posted By WaltL
I think you've posted in the wrong forum. There...

I think you've posted in the wrong forum. There is a SOLiD forum here.
Forum: 454 Pyrosequencing 12-03-2010, 11:16 AM
Replies: 2
Views: 3,254
Posted By WaltL
Yvan, Wish I had some good info for you. ...

Yvan,

Wish I had some good info for you. I'm still running Ver 2.3. My fix was to filter the data outside of Newbler and then do hybrid assemblies using fasta/qual data. Prior to that, I was...
Forum: 454 Pyrosequencing 04-05-2010, 08:15 AM
Replies: 2
Views: 3,254
Posted By WaltL
Newbler 2.3 on Ubuntu- Anyone?

I'm running Newbler 2.3 on an Ubuntu box (MacPro, dual quad core, 32 Gb RAM) and having some issues. Wondering if anyone out there is using Ubuntu and experiencing similar problems?

Everything...
Forum: 454 Pyrosequencing 01-14-2010, 06:01 AM
Replies: 3
Views: 1,870
Posted By WaltL
Good point! I got this ver. from our core...

Good point! I got this ver. from our core facility, so maybe they gave me the wrong install disk since this summer the Roche rep. said it was the latest "hot off the presses" version. I should be...
Forum: 454 Pyrosequencing 01-13-2010, 02:58 PM
Replies: 3
Views: 1,870
Posted By WaltL
Performing Hybrid Assemblies With Newbler

Has anyone performed assemblies with GSAssembler (ver. 2.0.01) using Sanger data (fasta) in combination with 454 data? A friend has done this for me with miraEST and I was going to try it with...
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