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Search: Posts Made By: lindseyjane
Forum: Bioinformatics 11-04-2010, 04:27 AM
Replies: 2
Views: 3,267
Posted By lindseyjane
Thank you, I did not know of this tool and it has...

Thank you, I did not know of this tool and it has been very helpful.
Forum: Bioinformatics 11-03-2010, 02:20 AM
Replies: 2
Views: 3,267
Posted By lindseyjane
problem with gsnap sam output

I have used the gsnap tool to align short reads against a reference and obtained sam output using the flag -A sam.
The sam file looks ok but when I try to convert it to a bam file then I get a...
Forum: Bioinformatics 11-02-2010, 12:57 AM
Replies: 13
Views: 3,830
Posted By lindseyjane
Thank you for your advice, I am checking out...

Thank you for your advice, I am checking out gsnap.
Forum: Bioinformatics 11-01-2010, 08:45 AM
Replies: 13
Views: 3,830
Posted By lindseyjane
Alignment tool for use with ambiguous reference?

Does anyone know of an alignment tool other than novoalign that we can use with a reference that contains ambiguity codes as well as A,G,C,Ts? Our aim is to do allele specific expression analysis so...
Forum: Bioinformatics 06-04-2010, 02:11 AM
Replies: 19
Views: 20,354
Posted By lindseyjane
Thanks very much webbrewer for your bioperl fix,...

Thanks very much webbrewer for your bioperl fix, it worked perfectly. :)
Forum: Bioinformatics 01-19-2010, 07:43 AM
Replies: 7
Views: 2,871
Posted By lindseyjane
Excellent idea, yes please! That would be so...

Excellent idea, yes please! That would be so useful.
Forum: Bioinformatics 01-19-2010, 02:00 AM
Replies: 7
Views: 2,871
Posted By lindseyjane
Thank you so very much for taking the time to...

Thank you so very much for taking the time to produce this code. It is an excellent starting point for me and I appreciate the time you have spent.

I hope soon I will be able to produce perl code...
Forum: Bioinformatics 01-17-2010, 11:47 PM
Replies: 7
Views: 2,871
Posted By lindseyjane
Yes, I am learning perl. Does anyone have an...

Yes, I am learning perl. Does anyone have an existing solution?
Forum: Bioinformatics 01-15-2010, 01:38 AM
Replies: 7
Views: 2,871
Posted By lindseyjane
How to calculate proportion of reads with each base at every reference position

I have a need to calculate the following, and wonder if anyone else has done something similar or could advise me on how to do it. The question is:

For each base position on a reference sequence,...
Forum: Bioinformatics 12-16-2009, 07:21 AM
Replies: 5
Views: 3,377
Posted By lindseyjane
Thanks for all your help and rapid responses to...

Thanks for all your help and rapid responses to my queries :)
Forum: Bioinformatics 12-16-2009, 06:22 AM
Replies: 5
Views: 3,377
Posted By lindseyjane
ok, thanks, I am learning to use perl, not...

ok, thanks, I am learning to use perl, not familiar with python, so I will write a script to do this in perl.

Just to clarify, do you know whether I need to alter the reverse read to make the...
Forum: Bioinformatics 12-16-2009, 02:38 AM
Replies: 5
Views: 3,377
Posted By lindseyjane
BFAST input format for paired end reads

I would like to know what I should do to input paired end reads to the BFAST software. The script provided, qseq2fastq.pl requires qseq files but I only have the sequence files from the Illumina...
Forum: Bioinformatics 11-02-2009, 01:01 AM
Replies: 514
Views: 213,228
Posted By lindseyjane
Question regarding bwt paired end alignment

I am currently trying to aligned paired end Illumina reads using bowtie and I want to compare the results to those from maq.

I cannot see an option for reporting an alignment for a read when its...
Forum: 454 Pyrosequencing 10-23-2009, 07:56 AM
Replies: 7
Views: 8,733
Posted By lindseyjane
Thank you for these pieces of advice, I will try...

Thank you for these pieces of advice, I will try all of these ...:)
Forum: Bioinformatics 10-22-2009, 05:19 AM
Replies: 3
Views: 2,357
Posted By lindseyjane
Mosaik assembler error

I am using the Mosaik assembler with some 454 reads and carried out the

MosaikBuild
MosaikAlign
MosaikSort

steps with no problems.
When I try to do the MosaikAssembler step I get the...
Forum: 454 Pyrosequencing 10-20-2009, 11:48 PM
Replies: 7
Views: 8,733
Posted By lindseyjane
How to get started analysing 454 data

I have got some data from a 454 titanium sequencing run (single end) of a model plant genome and the sequencing centre have provided us with the following files:

sff/library1. sff library2.sff...
Forum: Bioinformatics 09-21-2009, 01:36 AM
Replies: 3
Views: 3,485
Posted By lindseyjane
Thank you, problem solved:)

Thank you, problem solved:)
Forum: Bioinformatics 09-18-2009, 03:28 AM
Replies: 3
Views: 3,485
Posted By lindseyjane
problem using samtools tview viewer

Hello,

Has anyone had a problem using the samtools tview?

using the command

samtools tview sorted.bam ref.fa

I simply get a blank black screen and no display, no error message either.
Forum: Bioinformatics 09-17-2009, 01:27 AM
Replies: 5
Views: 2,414
Posted By lindseyjane
Thank you, I will try out these tools

Thank you, I will try out these tools
Forum: Bioinformatics 09-11-2009, 01:46 AM
Replies: 5
Views: 2,414
Posted By lindseyjane
How to visualise alignments with different read lengths?

Hi,

Does anyone know of a tool that can be used to view alignments of short reads to a reference when the short reads are of different lengths? We have 36bp and 51bp Illumina paired end read...
Forum: Bioinformatics 09-09-2009, 11:15 PM
Replies: 2
Views: 4,867
Posted By lindseyjane
Thank you :)

Thank you :)
Forum: Bioinformatics 09-09-2009, 10:58 AM
Replies: 2
Views: 4,867
Posted By lindseyjane
ABySS for paired reads?

Does anyone know whether or not a version of the ABySS software will be released in the future that can handle paired short reads?

I am trying to do a de novo short read assembly but the input...
Forum: Bioinformatics 08-13-2009, 08:15 AM
Replies: 99
Views: 41,506
Posted By lindseyjane
MapView not working for paired reads

Hello,

I would like to visualise some paired reads data using MapView. I have tried to use MVFmaker and choose the checkbox of Paired-end data. However, this checkbox is greyed out and I cannot...
Forum: Bioinformatics 07-28-2009, 02:19 AM
Replies: 22
Views: 8,577
Posted By lindseyjane
TopHat .sam output format not recognised

I am using TopHat v. 1.0.9 to analyse 36bp Illumina reads. The out put files .sam .wig and .bed have been generated successfully. I then try to view the SAM format results using the samtools and...
Forum: Literature Watch 06-09-2009, 06:20 AM
Replies: 0
Views: 1,967
Posted By lindseyjane
Genome assembly reborn: recent computational challenges

Briefings in Bioinformatics Advance Access originally published online on May 29, 2009
Briefings in Bioinformatics 2009 10(4):354-366; doi:10.1093/bib/bbp026

Genome assembly reborn: recent...
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