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Search: Posts Made By: JohnN
Forum: Bioinformatics 05-30-2017, 02:22 PM
Replies: 5
Views: 5,625
Posted By JohnN
You could alway try mauve aligner:...

You could alway try mauve aligner: http://darlinglab.org/mauve/mauve.html
Forum: Bioinformatics 12-06-2016, 10:58 AM
Replies: 13
Views: 2,426
Posted By JohnN
If you have lots of complete ORFs or genes, with...

If you have lots of complete ORFs or genes, with similar numbers to other members of the same species, with no gaps, you can be confident that you have a fairly completed genome considering your...
Forum: Bioinformatics 12-06-2016, 10:17 AM
Replies: 13
Views: 2,426
Posted By JohnN
How about annotating it with prokka and seeing...

How about annotating it with prokka and seeing what the ORF coverage to the DNA is via Artemis. Your genome could be diverged from the reference.
Forum: Bioinformatics 10-31-2014, 04:26 AM
Replies: 17
Views: 2,298
Posted By JohnN
Or just run it including the parameters in my...

Or just run it including the parameters in my previous post above, and Mira will accept the long file names.
Forum: Bioinformatics 10-30-2014, 10:03 AM
Replies: 17
Views: 2,298
Posted By JohnN
Or use: parameters = COMMON_SETTINGS...

Or use:

parameters = COMMON_SETTINGS -NW:mrnl=0

to parse long read names
Forum: Bioinformatics 10-30-2014, 09:58 AM
Replies: 5
Views: 2,001
Posted By JohnN
prokka uses Prodigal (http://prodigal.ornl.gov/)...

prokka uses Prodigal (http://prodigal.ornl.gov/) for its ORF predictions.
Forum: Bioinformatics 10-29-2014, 08:25 AM
Replies: 17
Views: 2,298
Posted By JohnN
Looking at your steps, the only place where the...

Looking at your steps, the only place where the read names could be messed up could be in your fna/qual to fastq conversion...

Could you not take the SFF files from the 454 assembly and convert...
Forum: Bioinformatics 10-28-2014, 06:25 AM
Replies: 17
Views: 2,298
Posted By JohnN
I'm not sure how to answer. Your read names...

I'm not sure how to answer. Your read names should not have any overlaps. How did you generate your fastq files? I tend to use mira's sff_extract. But there are lots of good sff extractors out...
Forum: Bioinformatics 10-27-2014, 10:01 AM
Replies: 17
Views: 2,298
Posted By JohnN
I'm wondering if the trimming process may not...

I'm wondering if the trimming process may not have clipped the read names - are you able to check that?

Also, mira works better if you do NOT preprocess your data - as mira will trim internally...
Forum: Bioinformatics 10-09-2014, 01:45 PM
Replies: 2
Views: 1,085
Posted By JohnN
You also, unless you really know what you are...

You also, unless you really know what you are doing, should consider not using sequence reads without quality data with Mira, unless you have chopped up a finished sequence and are doing something...
Forum: Bioinformatics 09-19-2014, 07:01 AM
Replies: 7
Views: 2,793
Posted By JohnN
There are several approaches of varying...

There are several approaches of varying complexity and cost:

The easiest in my recent experience, is to get PacBio sequencing done. With the illumina reads mapped to a PacBio assembly, you can...
Forum: Bioinformatics 07-21-2014, 01:12 PM
Replies: 12
Views: 4,010
Posted By JohnN
I recommend two things: 1. Try the mira list...

I recommend two things:

1. Try the mira list where they are very helpful: http://www.freelists.org/list/mira_talk

2. Ask your PacBio sequencing provider for the metadata.xml, bas.h5 and bax.h5...
Forum: Bioinformatics 07-11-2014, 12:00 PM
Replies: 13
Views: 3,341
Posted By JohnN
Put all of your contigs into a single fasta file...

Put all of your contigs into a single fasta file (or use the SAM or CAF file which an assembler spits out).

Then use the "tg_index" program which comes with the Staden package to make the gap5...
Forum: Bioinformatics 07-07-2014, 04:13 PM
Replies: 13
Views: 3,341
Posted By JohnN
The Staden package's gap5 is what I use.

The Staden package's gap5 is what I use.
Forum: Bioinformatics 07-02-2014, 07:53 AM
Replies: 2
Views: 2,822
Posted By JohnN
Maybe "bamtools" could help...

Maybe "bamtools" could help (https://github.com/pezmaster31/bamtools)

e.g. $ bamtools stats -n YourFile.bam


**********************************************
Stats for BAM file(s):...
Forum: Bioinformatics 03-05-2014, 06:10 PM
Replies: 3
Views: 1,282
Posted By JohnN
Google "prokka". It's straightforward to install...

Google "prokka". It's straightforward to install and run, but you need a unix box.
Forum: Bioinformatics 03-01-2014, 02:05 PM
Replies: 6
Views: 1,477
Posted By JohnN
How big is the string that you want to look for?...

How big is the string that you want to look for? Gene-sized? Use BLAST. A few to a few dozen nucleotides, "grep" or a string search tool would work.
Forum: Bioinformatics 02-07-2014, 02:47 PM
Replies: 8
Views: 1,874
Posted By JohnN
I wrote this a few years back. ...

I wrote this a few years back.

https://code.google.com/p/nash-bioinformatics-codelets/downloads/detail?name=subset_fasta.pl&can=2&q=
Forum: Bioinformatics 01-31-2014, 03:44 AM
Replies: 2
Views: 2,193
Posted By JohnN
I usually get some PCR sequenced.

I usually get some PCR sequenced.
Forum: Bioinformatics 12-11-2013, 10:58 AM
Replies: 2
Views: 1,826
Posted By JohnN
My advice would be to contact Eduardo and Peter...

My advice would be to contact Eduardo and Peter K. as they are very collaborative, smart and resourceful.
Forum: Bioinformatics 10-27-2013, 07:12 AM
Replies: 17
Views: 4,567
Posted By JohnN
Because on my heavy reliance on MacPorts, I'm...

Because on my heavy reliance on MacPorts, I'm waiting for verification that MacPorts works with Mavericks. (I have not checked since Friday).
Forum: Bioinformatics 08-13-2013, 10:16 AM
Replies: 9
Views: 4,369
Posted By JohnN
Try this:...

Try this: https://code.google.com/p/nash-bioinformatics-codelets/downloads/detail?name=subset_fasta.pl&can=2&q=

Hopefully it will do the job you need.

J
Forum: Bioinformatics 05-10-2013, 03:35 AM
Replies: 5
Views: 1,385
Posted By JohnN
Those questions are like going into a car...

Those questions are like going into a car dealership, buying a car, and saying "How do I drive?". They hint at no prior knowledge to build on. Answering them as asked will get you nowhere, and is...
Forum: Bioinformatics 04-03-2013, 04:20 PM
Replies: 14
Views: 9,937
Posted By JohnN
union from the EMBOSS suite will work, eg. ...

union from the EMBOSS suite will work, eg.

$ union -sequence FileA.gbk -sformat genbank -outseq FileB.gbk -osformat genbank -feature Y -auto
Forum: Bioinformatics 03-29-2013, 12:16 PM
Replies: 4
Views: 2,465
Posted By JohnN
To make it easy for lazy programmers like me to...

To make it easy for lazy programmers like me to know when bases have stopped and quality scores have started? Especially when line feeds can't be trusted?
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