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Forum: Bioinformatics 05-21-2015, 01:52 AM
Replies: 2
Views: 1,190
Posted By boetsie
The tool 'Bandage' can visualize assemblies from...

The tool 'Bandage' can visualize assemblies from SPAdes using the fastG format it produces. You can load the results of the final scaffolds or the intermediate K-mer contigs. Also, you can BLAST...
Forum: Bioinformatics 05-17-2015, 11:08 AM
Replies: 9
Views: 4,565
Posted By boetsie
The plot that Brian mentioned can be produced...

The plot that Brian mentioned can be produced with GAEMR (http://www.broadinstitute.org/software/gaemr/reference-manual/). See an example of the plot at Figure 6.1 'Blast Bubbles'
Forum: Bioinformatics 02-04-2015, 12:46 AM
Replies: 39
Views: 4,869
Posted By boetsie
If you do not mind to upload it to a server, you...

If you do not mind to upload it to a server, you can use NCBI's eukaryotic annotation pipeline;

http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/

If you just want to predict genes, go...
Forum: Bioinformatics 02-04-2015, 12:37 AM
Replies: 7
Views: 2,121
Posted By boetsie
Maybe this program will help: ...

Maybe this program will help:

https://github.com/svm-zhang/AGOUTI

I have not used it myself though.
Forum: Bioinformatics 12-31-2014, 01:47 AM
Replies: 252
Views: 98,599
Posted By boetsie
Hi Mattos LP, This should not be a problem,...

Hi Mattos LP,

This should not be a problem, as long as the input (contig) sequences are in fasta format. SSPACE tries to extend the end of the sequences using the unmapped sequence reads.
...
Forum: Introductions 12-08-2014, 12:56 AM
Replies: 3
Views: 928
Posted By boetsie
I think this paper is a good start to give you an...

I think this paper is a good start to give you an overview of the different stages of assembly, but also about pre and postprocessing;
...
Forum: Bioinformatics 06-06-2014, 02:03 AM
Replies: 3
Views: 1,326
Posted By boetsie
Strange indeed! You can also download it directly...

Strange indeed! You can also download it directly from the ftp here;

ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Bacteria/Campylobacter_coli_CVM_N29710_uid184035/

This .gbk file contains the...
Forum: Bioinformatics 02-27-2014, 02:49 AM
Replies: 252
Views: 98,599
Posted By boetsie
Sorry for the late reply. It seems that I do not...

Sorry for the late reply. It seems that I do not get an e-mail notification anymore when a reply is given in this thread :confused:

Please have a look at this post where colindaven suggests how to...
Forum: Bioinformatics 02-19-2014, 02:30 AM
Replies: 19
Views: 2,683
Posted By boetsie
Great, good luck with your analysis.

Great, good luck with your analysis.
Forum: Bioinformatics 02-19-2014, 02:09 AM
Replies: 19
Views: 2,683
Posted By boetsie
Here you go. You had a mistake in your code, you...

Here you go. You had a mistake in your code, you took the third column as your contig in this line;

my $contig = $s[2];

while the contig was in the second column.

In addition, since you only...
Forum: Bioinformatics 02-19-2014, 01:47 AM
Replies: 19
Views: 2,683
Posted By boetsie
I did not test it, but I think it would be...

I did not test it, but I think it would be something like this. Run it as;

perl script <samfile> <contigfile>


#!usr/bin/perl-w
use strict;
use warnings;

open(SAM,$ARGV[0]);
Forum: Bioinformatics 02-19-2014, 01:22 AM
Replies: 19
Views: 2,683
Posted By boetsie
PM me your code and the two input files, so I can...

PM me your code and the two input files, so I can help you with that..
Forum: Bioinformatics 02-19-2014, 01:16 AM
Replies: 19
Views: 2,683
Posted By boetsie
Yes. The first part (reading the mapped sam file)...

Yes. The first part (reading the mapped sam file) you should do yourself. But basically, this is what you already have. The second part (the code shown above) is for extracting the contig sequence.
Forum: Bioinformatics 02-19-2014, 12:59 AM
Replies: 19
Views: 2,683
Posted By boetsie
The error is caused, because in the corresponding...

The error is caused, because in the corresponding line you are refering to a hash ($seq{$_}), while you did not define a hash for seq in line 5;
my $seq = ();

In addition, your 'seq' hash is not...
Forum: Bioinformatics 02-04-2014, 01:45 PM
Replies: 2
Views: 1,713
Posted By boetsie
Use a tool like Prokka...

Use a tool like Prokka (http://www.vicbioinformatics.com/software.prokka.shtml) to predict and annotate your sequences. After the genbank or other files are generated, write a script to add the...
Forum: Bioinformatics 02-01-2014, 12:39 PM
Replies: 1
Views: 881
Posted By boetsie
YOu can try this tool; ...

YOu can try this tool;

http://www.vicbioinformatics.com/software.prokka.shtml
Forum: Bioinformatics 01-07-2014, 02:37 AM
Replies: 366
Views: 182,748
Posted By boetsie
Ha, I just wanted to post that blog prakhar! ...

Ha, I just wanted to post that blog prakhar!

In addition, the datasets from Illumina's BaseSpace are said to be publicly available; https://basespace.illumina.com/home/index
Forum: Bioinformatics 01-06-2014, 01:16 PM
Replies: 366
Views: 182,748
Posted By boetsie
That would be a great new feature Simon! There is...

That would be a great new feature Simon! There is a list of adapters at;
http://support.illumina.com/downloads/illumina_adapter_sequences_letter.ilmn

There are some datasets at the Illumina...
Forum: Bioinformatics 01-06-2014, 02:11 AM
Replies: 4
Views: 1,449
Posted By boetsie
If you just want an exact match of the 37bp,...

If you just want an exact match of the 37bp, simply use 'grep'.

If mismatches should be allowed, I think you can do this with bowtie2. Make an index of your 37bp sequence and align the...
Forum: Bioinformatics 01-01-2014, 10:02 AM
Replies: 2
Views: 2,001
Posted By boetsie
Prokka is a pipeline to predict genomic elements,...

Prokka is a pipeline to predict genomic elements, such as genes, rRNA, tRNA and non-coding RNA. In addition, it annotates the genes with BLAST against the swissprot database and other databases....
Forum: Bioinformatics 12-27-2013, 02:25 PM
Replies: 4
Views: 2,581
Posted By boetsie
You can align your five genes to the scaffolds...

You can align your five genes to the scaffolds with Nucmer (part of MUMmer);

http://mummer.sourceforge.net/
Forum: Bioinformatics 12-16-2013, 01:51 PM
Replies: 18
Views: 5,294
Posted By boetsie
Only thing I know is that the last column is...

Only thing I know is that the last column is referenced to the file 'organism_map'. In this case;

382680 uncultured bacterium 77133

The number 77133 is a taxonomy number, which you can...
Forum: Bioinformatics 12-16-2013, 01:32 PM
Replies: 4
Views: 5,439
Posted By boetsie
You can use a tool like barrnap ...

You can use a tool like barrnap

http://www.vicbioinformatics.com/software.barrnap.shtml
or RNAmmer
http://www.cbs.dtu.dk/services/RNAmmer/

to predict rRNA locations on your contig...
Forum: Bioinformatics 12-16-2013, 06:47 AM
Replies: 3
Views: 5,059
Posted By boetsie
Have a look at RiboPicker: ...

Have a look at RiboPicker:

http://ribopicker.sourceforge.net/

You can download the tool and rRNA databases. It uses a modified version of bwa-sw for alignment against a rRNA database and splits...
Forum: Bioinformatics 12-12-2013, 04:13 AM
Replies: 18
Views: 5,294
Posted By boetsie
I've already figured that out :) Thanks for your...

I've already figured that out :) Thanks for your help though!
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