Forum: Bioinformatics
07-02-2015, 06:19 PM
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Replies: 0
Views: 1,850
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Forum: Bioinformatics
03-19-2014, 10:59 AM
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Replies: 3
Views: 2,779
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Forum: Bioinformatics
03-19-2014, 08:58 AM
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Replies: 3
Views: 2,779
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...
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Forum: Bioinformatics
03-06-2014, 08:59 AM
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Replies: 3
Views: 1,796
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...
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Forum: Bioinformatics
02-19-2014, 01:42 PM
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Replies: 3
Views: 3,529
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Forum: Bioinformatics
02-07-2014, 06:15 AM
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Replies: 4
Views: 2,204
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Forum: Bioinformatics
02-06-2014, 02:50 PM
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Replies: 4
Views: 2,204
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Forum: Bioinformatics
02-06-2014, 02:47 PM
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Replies: 4
Views: 2,204
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Forum: Bioinformatics
12-04-2013, 06:56 AM
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Replies: 3
Views: 4,910
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...
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Forum: Bioinformatics
12-03-2013, 07:23 PM
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Replies: 3
Views: 4,910
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...
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Forum: Illumina/Solexa
10-21-2013, 11:05 AM
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Replies: 2
Views: 3,032
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...
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Forum: Bioinformatics
08-22-2013, 08:09 AM
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Replies: 2
Views: 1,726
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.
...
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Forum: Bioinformatics
08-15-2013, 06:20 AM
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Replies: 4
Views: 1,741
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...
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Forum: Bioinformatics
08-14-2013, 09:24 AM
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Replies: 4
Views: 1,741
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...
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Forum: Bioinformatics
07-15-2013, 10:55 AM
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Replies: 1
Views: 1,374
"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...
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Forum: Bioinformatics
07-15-2013, 09:52 AM
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Replies: 5
Views: 1,903
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Forum: Bioinformatics
07-12-2013, 01:41 PM
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Replies: 5
Views: 1,903
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...
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Forum: Bioinformatics
07-12-2013, 12:25 PM
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Replies: 1
Views: 2,723
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...
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Forum: Bioinformatics
07-12-2013, 06:20 AM
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Replies: 5
Views: 1,903
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Forum: Bioinformatics
07-12-2013, 06:00 AM
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Replies: 2
Views: 1,229
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Forum: Bioinformatics
07-11-2013, 01:20 PM
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Replies: 5
Views: 1,903
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...
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Forum: Bioinformatics
06-26-2013, 01:47 PM
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Replies: 2
Views: 1,229
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...
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Forum: Bioinformatics
06-19-2013, 08:13 AM
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Replies: 2
Views: 2,310
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...
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Forum: Introductions
06-19-2013, 06:20 AM
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Replies: 0
Views: 649
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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