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Search: Posts Made By: niazi84@hotmail.com
Forum: Bioinformatics 09-21-2015, 01:47 AM
Replies: 0
Views: 1,078
DEXSeq analysis does not complete

Hi all,

I am having problem in diff. exon usage analysis of my dataset. I generated count data using protocol mentioned in DEXSeq's manual. My runs seem to be halted after some time when DEXSeq...
Forum: Bioinformatics 11-28-2012, 10:00 AM
Replies: 5
Views: 2,074
hello, I also want to do the same but could...

hello,

I also want to do the same but could not find any software. Did you find any overlaping assembler?
Forum: RNA Sequencing 05-01-2011, 05:10 PM
Replies: 15
Views: 6,427
i want to use Orpheus and Z-curve along with it...

i want to use Orpheus and Z-curve along with it but unable to find it anywhere on the web. Did you use it? Can you tell from where i can download these two.

regards,
adnan
Forum: Bioinformatics 01-06-2011, 10:31 AM
Replies: 2
Views: 2,720
Hi Navin, I am also looking for such...

Hi Navin,

I am also looking for such software or script. Did you find any till now?
Forum: General 04-02-2010, 09:53 AM
Replies: 2
Views: 17,462
Hi, I have illumina multiplex paired end...

Hi,

I have illumina multiplex paired end data of 75bp. The insert size 300-400bp including primer and adapter sequences. I want to check whether my data contains adapter sequence or not for that i...
Forum: De novo discovery 02-24-2010, 05:22 AM
Replies: 37
Views: 19,229
Marten, you can use Bambus 2.33 by AMOS. It takes...

Marten, you can use Bambus 2.33 by AMOS. It takes contig and mate file as input. I am also trying to use it but i dont have mate file as required by Bambus. DO you know how to create mate file? I...
Forum: De novo discovery 02-24-2010, 02:19 AM
Replies: 6
Views: 6,047
But Bambus needs contig and mate information...

But Bambus needs contig and mate information files as input. I have ace which i can convert to contig files "ace2contig" but how to get "mate file"?
Forum: Bioinformatics 02-19-2010, 08:36 AM
Replies: 8
Views: 3,429
Also how i convert paired end reads in .afg...

Also how i convert paired end reads in .afg format since nowhere on AMOS pages is mentioned about paired end reads conversion. I am gone mad in this, no help on the web and at AMOS-help.
Forum: Bioinformatics 02-19-2010, 01:41 AM
Replies: 8
Views: 3,429
Thanks johnson. I am actually intending to do...

Thanks johnson. I am actually intending to do comparative assembly of bacterial strain whose data is from illumina GA2 with 75bp of reads. The data was in scarf format and i converted it into...
Forum: Bioinformatics 02-15-2010, 04:10 PM
Replies: 8
Views: 3,429
i have installed AMOS but i dont know how to make...

i have installed AMOS but i dont know how to make relevant input formats from illumina reads and reference sequence.
Forum: Bioinformatics 02-15-2010, 03:32 AM
Replies: 8
Views: 3,429
HI Patrick, Did you get any assistance about...

HI Patrick,

Did you get any assistance about AMOS. I am at the same position when you did this post. Any help you can do?
Forum: Bioinformatics 02-15-2010, 01:43 AM
Replies: 27
Views: 12,011
Thanks for reply Bio-x but i have been assigned...

Thanks for reply Bio-x but i have been assigned to do comparative assembly not denovo but i can try after it. But first i want to look at AMOS since it took 6 banging days to install it and now i...
Forum: Bioinformatics 02-14-2010, 07:07 AM
Replies: 27
Views: 12,011
AMOS Input Files

Anyone has tried running sequence data in AMOS. I am unable to find the way to start after installing AMOS since the documentation is so unorganized. I have paried end data from illumina 75bp. Can...
Forum: De novo discovery 02-09-2010, 02:38 PM
Replies: 6
Views: 6,047
Need Help

I know its too long to ask but i need help. Which software you use for scaffolding, was it Bambus? I am using Mosaik, a comparative assembler which generates .ace file (consensus). Can i use Bambus...
Forum: Bioinformatics 02-09-2010, 02:23 PM
Replies: 15
Views: 7,254
I think you are talking about using 'pileup'...

I think you are talking about using 'pileup' command with -c (consensus calling parameter). Am i right?

I also have .ace file from mosaik but i dont know whats the next step to do with it. Can you...
Forum: Illumina/Solexa 02-08-2010, 09:27 AM
Replies: 3
Views: 5,077
Smile Thank you very much. It worked for me But if i...

Thank you very much. It worked for me But if i am not bothering, can you tell what is the problem with symbolic format and fq_allstd.pl doesnt convert it as it is provided by along with data for...
Forum: Bioinformatics 02-08-2010, 03:20 AM
Replies: 21
Views: 33,040
@hannat.. Did you get the solution of your...

@hannat..

Did you get the solution of your problem. I have same kind of problem with my data.

Thanks
Forum: Illumina/Solexa 02-08-2010, 02:53 AM
Replies: 3
Views: 5,077
hello, Long time passed for this question....

hello,

Long time passed for this question. Did you get the solution for your question?

Thanks
Forum: Bioinformatics 02-06-2010, 03:56 AM
Replies: 2
Views: 3,160
Thans tata, its good reference. I used Maq...

Thans tata,

its good reference. I used Maq for assembly today and got the consensus sequence finally in .cns file. Now what should be done next to refine the sequence and which tools, any idea?
...
Forum: Bioinformatics 02-05-2010, 04:07 AM
Replies: 2
Views: 3,160
Steps to Genome Assembly??

Hello,
I am a newbie to genome assembling. Can anybody help me knowing because i am gone mad after reading about assembly and alignment in articles but couldn't get anything out. My main questions...
Forum: Bioinformatics 02-05-2010, 03:24 AM
Replies: 78
Views: 43,877
Thanks for quick reply. I want to do comparative...

Thanks for quick reply. I want to do comparative assembly and at the moment using mozaik for that which generates .ace file (.sam & .bam are optional). Can we use GAP5 for viewing, editing and...
Forum: Bioinformatics 02-05-2010, 02:53 AM
Replies: 78
Views: 43,877
Is it comparative or denovo

Hi,

I am new to all this. Can anybody tell me, STADEN package does comparative assembly or de novo assembly? Thanks
Forum: SOLiD 02-02-2010, 12:43 PM
Replies: 3
Views: 2,894
How to view output

Hello,

I am new to BFast. I have executed the sample data from tutorial's commands. Now i have .sam reported file. Can anybody tell me how to view this file. Will i have to use other software to...
Forum: Introductions 02-02-2010, 12:34 AM
Replies: 3
Views: 1,268
Great :) I am looking for mapping/reference based...

Great :) I am looking for mapping/reference based assembly software for bacterial genome. Have you any idea which one is better to use, coz Velvet and SSake does de novo assembly. Any idea ???
Forum: Introductions 02-01-2010, 04:25 PM
Replies: 3
Views: 1,268
Hello Jose! I am new and also searching some...

Hello Jose!
I am new and also searching some good free softwares for assembly of genomes from solexa reads. Yes, these softwares requires lot of memory. I think atleast Mac's 3 GHz processor, 12 GB...
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