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Search: Posts Made By: pari_89
Forum: Bioinformatics 08-06-2013, 01:56 AM
Replies: 8
Views: 9,902
Posted By pari_89
Hi there, I think you are running the command...

Hi there, I think you are running the command wrongly. The command in the documentation says this :

mummerplot -x "[0,275287]" -y "[0,265111]" -postscript -p mummer mummer.mums

-x and - y are...
Forum: De novo discovery 07-30-2013, 03:01 AM
Replies: 4
Views: 5,518
Posted By pari_89
You can take a look at QUAST as well. It computes...

You can take a look at QUAST as well. It computes all the metrics.

http://sourceforge.net/projects/quast/
Forum: Bioinformatics 07-19-2013, 07:32 AM
Replies: 1
Views: 940
Posted By pari_89
Denovo Versus Mapping

Hi everyone, I wanted to compare the time and efficiency of de-novo v/s mapping assembly.

Can anyone refer me to a paper where I can get an idea which is more time consuming or memory intensive...
Forum: Bioinformatics 07-17-2013, 11:52 PM
Replies: 12
Views: 9,943
Posted By pari_89
hi everyone, I am currently using mira for a...

hi everyone, I am currently using mira for a mapping assembly. My manifest file is like this :
project = bsb_assembly
job = genome,mapping,accurate
parameters = -GE:not=8

# The second part...
Forum: Bioinformatics 07-15-2013, 01:37 PM
Replies: 1
Views: 1,547
Posted By pari_89
QUAST GFF files for genes

Hi everyone, I am using QUAST to evaluate my assemblies. I have two annotated reference genomes and they are found in genbank. QUAST takes gff files for genes and operons and I would like to know...
Forum: Bioinformatics 07-15-2013, 03:24 AM
Replies: 15
Views: 20,662
Posted By pari_89
Hello, I have a similar question like but...

Hello, I have a similar question like but regarding mapping and Assembly. From literature, I have seen that there are 2 types of assemblies - denovo and assembly against a reference. The problem is...
Forum: Bioinformatics 07-14-2013, 02:48 AM
Replies: 1
Views: 786
Posted By pari_89
Genome_Coverage after assembly

Hi, I am probably asking a very basic question. I have assembled raw Ion Torrent reads from different tools to produce contigs. I have a reference genome, I want to know how to calculate the genome...
Forum: Bioinformatics 07-12-2013, 01:44 PM
Replies: 14
Views: 2,739
Posted By pari_89
Hi, thanks. I have a single fastQ file and the...

Hi, thanks. I have a single fastQ file and the first line is like this:

@VW27N:4:11...
Forum: Bioinformatics 07-12-2013, 11:15 AM
Replies: 14
Views: 2,739
Posted By pari_89
Hi, but can I use the fastQ file to see whether...

Hi, but can I use the fastQ file to see whether they are single or paired end reads? How do I know that?
Forum: Bioinformatics 07-12-2013, 06:36 AM
Replies: 14
Views: 2,739
Posted By pari_89
Hi everyone, I am probably asking a very basic...

Hi everyone, I am probably asking a very basic question. I have FastQ file from ion Torrent PGM sequencer and do not know whether the data is single read or paired end. How can I check for that? I...
Forum: Ion Torrent 07-07-2013, 04:23 PM
Replies: 27
Views: 19,230
Posted By pari_89
Hi, for ion torrent data, and de-novo assemblies...

Hi, for ion torrent data, and de-novo assemblies - CLCworkbench, Newbler, Ray, Mira and CAP3 are very good assemblers. I have tried them all and they work very well.

Now for mapping assemblies...
Forum: Bioinformatics 07-06-2013, 03:26 AM
Replies: 1
Views: 1,412
Posted By pari_89
Gage-b

Hello everyone, there is this new evaluation tool for bacterial genome assembly called GAGE-B.

The reference to the paper is :...
Forum: UK - Cambridge 07-04-2013, 12:46 PM
Replies: 2
Views: 7,630
Posted By pari_89
Hi, I am struggling with the same problem. But I...

Hi, I am struggling with the same problem. But I am using QUAST which gives n50 length and other metrics
Forum: Bioinformatics 07-04-2013, 12:45 PM
Replies: 2
Views: 874
Posted By pari_89
Contigs_Genes_deNovo assembly

Hello Everyone, I need have a set of contigs from de-novo assembly and would like to find the genes from the set of contigs and match them to a reference sequence.

If there are large amount of...
Forum: Bioinformatics 07-04-2013, 12:43 PM
Replies: 6
Views: 2,359
Posted By pari_89
Hi, I fixed the problem. Actually, the FASTA file...

Hi, I fixed the problem. Actually, the FASTA file was exported on a windows platform and I was running mummer on linux. I just copied the fasta file contents in a linux editor. It parsed the file...
Forum: Bioinformatics 07-01-2013, 10:21 AM
Replies: 2
Views: 719
Posted By pari_89
Mapping_assemblies

Hello every one, I have used gsMapper of Newbler, CLC workbench and Mira to assemble against a reference. These have produced contigs and I want to have a metric in order to assess the quality.
...
Forum: Bioinformatics 07-01-2013, 09:32 AM
Replies: 2
Views: 1,508
Posted By pari_89
Hi thanks a lot. I was not aware of those tools....

Hi thanks a lot. I was not aware of those tools. I wanted to try some of them but the problem is that the only file that my assemblers produce in common are contigs. CLC has its own viewer, RAy does...
Forum: Bioinformatics 07-01-2013, 03:54 AM
Replies: 8
Views: 9,902
Posted By pari_89
Hi, can you please tell me how you plotted the...

Hi, can you please tell me how you plotted the nucmer.delta file using mummer please?? I mean which commands did you use. I am trying to map contigs to a reference sequence.

THank you.
Forum: Bioinformatics 06-27-2013, 07:58 AM
Replies: 1
Views: 1,063
Posted By pari_89
Assembling against a reference

Hello everyone,

I have been doing some reading about mapping and assembling against a reference and I cannot quite understand the difference? What I understand it that mapping against a reference...
Forum: Bioinformatics 06-26-2013, 11:14 AM
Replies: 2
Views: 1,286
Posted By pari_89
OSLAY blast file

Hi, I am trying to use OSLAY (http://ab.inf.uni-tuebingen.de/software/oslay/)

but it is asking me for a blast matches file. How can I get the blast file. I have a set of contigs from different...
Forum: Bioinformatics 06-26-2013, 05:45 AM
Replies: 2
Views: 1,508
Posted By pari_89
Contig_Analysis

Hi everyone, I have used a series of de-novo tools and generated contigs from each one of them. I have used QUAST to assess the quality of assembly but QUAST does not display alignments which I would...
Forum: Bioinformatics 06-25-2013, 12:29 PM
Replies: 17
Views: 11,021
Posted By pari_89
Hello, I am trying to install amos-cmp version...

Hello, I am trying to install amos-cmp version 3.1.0 as well. Can you please tell me where to download and how to install those packages:

WARNING! BLAT was not found but is required to run...
Forum: De novo discovery 06-25-2013, 10:49 AM
Replies: 5
Views: 8,462
Posted By pari_89
Hi, Newbler performs reference-guided assembly. I...

Hi, Newbler performs reference-guided assembly. I ran it from the command line. It is runMapper option.

Hope this helps
Forum: Bioinformatics 06-25-2013, 07:54 AM
Replies: 12
Views: 9,943
Posted By pari_89
Thanks for the link. I will try the new version...

Thanks for the link. I will try the new version as well but since I am doing some research on the previous version I was wondering if anyone has the exact command lines.

I just want to map one...
Forum: Bioinformatics 06-24-2013, 12:33 PM
Replies: 3
Views: 4,169
Posted By pari_89
Can you please give me the link where mapping...

Can you please give me the link where mapping assembly instruction was given for mira?
I want to assemble reads against reference using iontorrent data.

THank you.
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