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Forum: Bioinformatics 07-02-2015, 07:19 PM
Replies: 0
Views: 1,801
Posted By akjones
How to Print Statistics from Python filtering script

Hello all,

I have the following python script which will filter paired-end fastq read data based on nucleotide complexity with a user provided percentage (as a way of removing reads with lots of...
Forum: Bioinformatics 03-19-2014, 11:59 AM
Replies: 3
Views: 2,690
Posted By akjones
Sorry, it wasn't enclosed because as of right now...

Sorry, it wasn't enclosed because as of right now it doesn't do anything other than read the file, so I didn't think posting it would be helpful. I don't know how to go about solving the other...
Forum: Bioinformatics 03-19-2014, 09:58 AM
Replies: 3
Views: 2,690
Posted By akjones
Question sort contigs based on fasta header

Hello All,

I have a problem that I am looking for some input on.

I have been using the genome assembler SPAdes, which outputs assembled contigs as a fasta file. I would like to sort my...
Forum: Bioinformatics 03-06-2014, 09:59 AM
Replies: 3
Views: 1,743
Posted By akjones
REAPR instruction manual?

Hello all,

I recently read the paper describing REAPR for De Novo genome assembly assessment and I would like to use it. However, I cannot find an actual download/instruction manual for the...
Forum: Bioinformatics 02-19-2014, 02:42 PM
Replies: 3
Views: 3,425
Posted By akjones
Question Help installing QUAST(quality assessment tool for genome assemblies)

Hello all,

I'm having some problems with installing QUAST and I'm hoping someone out there can help. So here's the deal:

I am trying to install QUAST on my Mac (OS 10.7.5). I have xcode and...
Forum: Bioinformatics 02-07-2014, 07:15 AM
Replies: 4
Views: 2,123
Posted By akjones
Thanks mastal, it's reassuring to hear they don't...

Thanks mastal, it's reassuring to hear they don't look too bad. My thoughts were similar with regards to the assembly. Do you know if there is a way to trim a specified number of bases from the 3'...
Forum: Bioinformatics 02-06-2014, 03:50 PM
Replies: 4
Views: 2,123
Posted By akjones
I couldn't fit all attachments, here are the 4...

I couldn't fit all attachments, here are the 4 for the stringent trim. R1 and R2 are from the left and right, respectively.

~Ana
Forum: Bioinformatics 02-06-2014, 03:47 PM
Replies: 4
Views: 2,123
Posted By akjones
FastQC analyses of trimmed MiSeq reads kmer content

Hello all,

After doing quite a bit of "lurking" with regards to other posts on this topic I have found that although my problem/question is similar to others out there, it is not the same so I...
Forum: Bioinformatics 12-04-2013, 07:56 AM
Replies: 3
Views: 4,817
Posted By akjones
Hi Dario, Thanks very much, your code...

Hi Dario,

Thanks very much, your code works! What do you mean by are you referring to the direction of the reads (5'-3' or 3'-5') or the order of the reads themselves, as in read 1 followed by...
Forum: Bioinformatics 12-03-2013, 08:23 PM
Replies: 3
Views: 4,817
Posted By akjones
Question Code to split paired end MiSeq data?

Hello all,

I have some paired end MiSeq data that I have cleaned/trimmed. However the software I used to clean everything up requires that the paired end data files be concatenated into one fastq...
Forum: Illumina/Solexa 10-21-2013, 12:05 PM
Replies: 2
Views: 2,953
Posted By akjones
Question Media a potential source of DNA contamination?

Hi Everyone,

I am going to try to make this long story short and sweet. I have an environmental bacterial isolate that I would like to sequence the genome of using the Illumina MiSeq. It was very...
Forum: Bioinformatics 08-22-2013, 09:09 AM
Replies: 2
Views: 1,691
Posted By akjones
Trimming MiSeq data

Hello all,

Suggestions for any open source software for trimming/cleaning MiSeq data? I was thinking of giving Cutadapt a try but I would like to know what others have had success with.

...
Forum: Bioinformatics 08-15-2013, 07:20 AM
Replies: 4
Views: 1,706
Posted By akjones
Thanks, GenoMax! Do you have any suggestions...

Thanks, GenoMax! Do you have any suggestions about how to convert the .crunch file and what format I should convert it to? My instinct is to go straight to a fasta file, but since the output from...
Forum: Bioinformatics 08-14-2013, 10:24 AM
Replies: 4
Views: 1,706
Posted By akjones
Question Genome viewer less clunky than ACT/Artemis?

Hello,

I'm wondering if anyone has any suggestions for a genome viewer other than ACT/Artemis? I have tried using ACT in the past but the software and layout is very clunky and I don't find it...
Forum: Bioinformatics 07-15-2013, 11:55 AM
Replies: 1
Views: 1,329
Posted By akjones
Question "uninitialized value" in ABACAS

Hello all,

I've recently starting working with ABACAS as part of the PAGIT suite of programs. After one run with altered parameters for identity, word size etc. in nucmer I got this printed in my...
Forum: Bioinformatics 07-15-2013, 10:52 AM
Replies: 5
Views: 1,862
Posted By akjones
Alright, fixed keyboard problems and changed the...

Alright, fixed keyboard problems and changed the discussed promer values to match the nucmer values, still got the same error. So if you could send the fixed file or put it on the pagit webpage that...
Forum: Bioinformatics 07-12-2013, 02:41 PM
Replies: 5
Views: 1,862
Posted By akjones
Thomas, I followed your suggestion and was...

Thomas,

I followed your suggestion and was able to view both the nucmer and promer files, I used the command "v" in "less" to allow me to edit. However, when I did this something very bizarre...
Forum: Bioinformatics 07-12-2013, 01:25 PM
Replies: 1
Views: 2,631
Posted By akjones
Hello, I realize this is an old post and...

Hello,

I realize this is an old post and you have probably long since either solved the problem or given up, but you can download and run ABACAS/ the entire PAGIT suite on a virtual machine using...
Forum: Bioinformatics 07-12-2013, 07:20 AM
Replies: 5
Views: 1,862
Posted By akjones
Thanks very much, I will give that a shot!

Thanks very much, I will give that a shot!
Forum: Bioinformatics 07-12-2013, 07:00 AM
Replies: 2
Views: 1,195
Posted By akjones
Hi Thomas, I did figure out the...

Hi Thomas,

I did figure out the installation part, but thanks for your reply. :)
Forum: Bioinformatics 07-11-2013, 02:20 PM
Replies: 5
Views: 1,862
Posted By akjones
Question Using PROmer as part of ABACAS (PAGIT)

Hi all,

I have recently installed PAGIT on Mac OSX and am working with ABACAS. So far I have gotten abacas to run using the default parameter settings and NUCmer. The command I entered was...
Forum: Bioinformatics 06-26-2013, 02:47 PM
Replies: 2
Views: 1,195
Posted By akjones
PAGIT Installation for Mac

Hello all,

I am trying to install PAGIT onto my Mac (OSX 10.7.5). The instructions on the Sanger website (http://www.sanger.ac.uk/resources/software/pagit/) say to install a virtual box first, I...
Forum: Bioinformatics 06-19-2013, 09:13 AM
Replies: 2
Views: 2,275
Posted By akjones
Genome Gap Closing/Finishing Software

Hi all,

I am working with the genome of a Gram- bacterium, ~3.6Mb. The genome was sequenced using an Illumina MiSeq platform with paired-end reads and a de novo assembly was done using CLC...
Forum: Introductions 06-19-2013, 07:20 AM
Replies: 0
Views: 637
Posted By akjones
Hello :)

Hello from Providence, RI. :) I am first year MS student working on the isolation and characterization of novel diazotrophs in estuarine sediments. At the moment I am primarily concerned with...
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