Software packages capable of aligning roughly 9000 bp

josecolquitt · 05-17-2010, 09:25 AM

I am currently working

peromhc · 05-17-2010, 02:04 PM

you'll probably need to give a few more details if you expect to get any help.. I this one 9000bp contig, 900 100bp Illumina reads, something else?

To what genome are you trying to align these bases?

lh3 · 05-17-2010, 05:42 PM

bwasw. it works for 100bp-100kbp, against the human genome.

NGSfan · 05-18-2010, 04:30 AM

Quote:

Originally Posted by josecolquitt

I am currently working

While the topic is interesting - I think your forum etiquette is a bit... well let's just say it's unconventional. You'll have to be more specific than that if you want to engage with others and get feedback.

On a side note - it is nice to see there are aligners that can handle longer reads, considering what the future brings!

josecolquitt · 05-18-2010, 05:17 AM

My apologies, I was attempting to delete the entire entry and revise. I am currently working with Simian Immunodeficiency Virus short reads obtained from 454. I am working at an internship trying to gain experience in the bioinformatics field. I am trying to use the Mosaik package in an attempt to sequence these short reads. However, I am having problems with the initialization of this package. Inside the read-me is a tutorial of sorts that guides the user through a demo of the command lists, and then gives a tutorial working with a sample set of C. elegans chromosome 2 reads.

When I attempt to click on any of the programs within the bin directory, a pop up window will display for a fraction of a second and then disappear. I am quite sure that this is simply a result of my inexperience with these programs. Any help or guidance would be greatly appreciated.

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05-17-2010, 09:25 AM	#1
josecolquitt Junior Member Location: South Carolina Join Date: May 2010 Posts: 4	Software packages capable of aligning roughly 9000 bp I am currently working Last edited by josecolquitt; 05-17-2010 at 12:03 PM.

05-18-2010, 05:17 AM	#5
josecolquitt Junior Member Location: South Carolina Join Date: May 2010 Posts: 4	Problems with Mosaik package My apologies, I was attempting to delete the entire entry and revise. I am currently working with Simian Immunodeficiency Virus short reads obtained from 454. I am working at an internship trying to gain experience in the bioinformatics field. I am trying to use the Mosaik package in an attempt to sequence these short reads. However, I am having problems with the initialization of this package. Inside the read-me is a tutorial of sorts that guides the user through a demo of the command lists, and then gives a tutorial working with a sample set of C. elegans chromosome 2 reads. When I attempt to click on any of the programs within the bin directory, a pop up window will display for a fraction of a second and then disappear. I am quite sure that this is simply a result of my inexperience with these programs. Any help or guidance would be greatly appreciated.

05-17-2010, 02:04 PM	#2
peromhc Senior Member Location: Durham, NH Join Date: Sep 2009 Posts: 108	you'll probably need to give a few more details if you expect to get any help.. I this one 9000bp contig, 900 100bp Illumina reads, something else? To what genome are you trying to align these bases?

05-17-2010, 05:42 PM	#3
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	bwasw. it works for 100bp-100kbp, against the human genome.