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Search: Posts Made By: R diggity
Forum: General 08-05-2010, 06:50 PM
Replies: 12
Views: 3,120
Posted By R diggity
Thanks to everyone for the suggestions so far. ...

Thanks to everyone for the suggestions so far. I've learned more in the past week than when I started looking at this project several months ago.

So, after mapping reads with Maq under many...
Forum: General 08-05-2010, 05:28 PM
Replies: 1
Views: 1,524
Posted By R diggity
It looks like this thread fell under the radar,...

It looks like this thread fell under the radar, but I too am facing a similar project. Is there anything like this in the literature? I've looked, but haven't had much luck.
Forum: General 08-05-2010, 10:05 AM
Replies: 12
Views: 3,120
Posted By R diggity
Thanks for explaining how to use the script! I...

Thanks for explaining how to use the script! I used ill2sanger successfully.

Original read qualities:

\^][Iba[GTVIYXYUUZ\VY^IXa`\_TGRIIZY]RDFY\][BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

Converted...
Forum: General 08-05-2010, 07:34 AM
Replies: 12
Views: 3,120
Posted By R diggity
FastQC also looks like a great way to evaluate...

FastQC also looks like a great way to evaluate reads, thanks. Does the sol2sanger script properly convert 1.5 illumina formats? I've tested it out and had slightly better alignment, but I thought...
Forum: General 08-04-2010, 02:59 PM
Replies: 12
Views: 3,120
Posted By R diggity
Ah, thanks for the lead. It appears as though I...

Ah, thanks for the lead. It appears as though I do have Illumina 1.5+. I'm not certain I understand how to run the scripts to convert these reads. Can I place the code within an existing Maq...
Forum: General 08-04-2010, 10:01 AM
Replies: 12
Views: 3,120
Posted By R diggity
Thanks for directing me towards PIQA, that's...

Thanks for directing me towards PIQA, that's exactly the sort of package I was looking for. I can't seem to get it to work, but for now I'm using Maq's built-in read length feature to "shorten"...
Forum: General 07-23-2010, 07:02 AM
Replies: 12
Views: 3,120
Posted By R diggity
Comparative genome analysis (using illumina reads)

Hi all,

I'm involved in a project involving SNP detection for various candidate genes. I've started by using Maq to align my reads using a mismatch value of 3. For some reason, I've only been...
Forum: Bioinformatics 07-10-2010, 11:40 AM
Replies: 3
Views: 1,808
Posted By R diggity
Thanks for the advice. I suppose I will have to...

Thanks for the advice. I suppose I will have to construct my reference genome from quite a few separate linkage groups. Given that my reads are 75bp in length, will I have to manually manipulate...
Forum: Bioinformatics 07-03-2010, 12:32 PM
Replies: 3
Views: 1,808
Posted By R diggity
Aligning numerous reads to several small references

Hi all,

I'm trying to assemble a large set of illumina reads (over 18 million) to a reference. My reference consists of multiple candidate sequences varying in size and location across the...
Forum: Bioinformatics 07-01-2010, 04:24 AM
Replies: 12
Views: 2,916
Posted By R diggity
Thanks for the advice raela. I checked and it...

Thanks for the advice raela. I checked and it looks like I'm using the correct version:

/usr/local/bin/maq: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared...
Forum: Bioinformatics 06-30-2010, 01:22 PM
Replies: 12
Views: 2,916
Posted By R diggity
http://www.ncbi.nlm.nih.gov/nuccore/NC_000962 ...

http://www.ncbi.nlm.nih.gov/nuccore/NC_000962

So this is a test reference I've tried. If I remove the "simustat" line in the maqdemo script the run actually finishes. Does anyone know the cause...
Forum: Bioinformatics 06-30-2010, 12:50 PM
Replies: 12
Views: 2,916
Posted By R diggity
I'm having the same problem running on 64 bit...

I'm having the same problem running on 64 bit Ubuntu 10.04. I've copied the necessary files into usr/local/bin and the simulation seems to work up until the same point as yuanlang posted.
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