SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 49
Search took 0.02 seconds.
Search: Posts Made By: damiankao
Forum: Bioinformatics 02-04-2015, 01:21 PM
Replies: 45
Views: 16,543
Posted By damiankao
Hi Brian, This tool looks great. Is there a...

Hi Brian,

This tool looks great. Is there a way to accept multiple fastq.gz files for inputs? I want to run all my reads (multiple fastq.gz) through bbnorm.
Forum: General 03-23-2012, 10:20 AM
Replies: 51
Sticky: NGS Blogs
Views: 48,138
Posted By damiankao
I started a blog recently: ...

I started a blog recently:
blog.nextgenetics.net

I've written some entries on GO analysis and data visualization using javascript. I am not a veteran of the field, just a phd student. Hopefully...
Forum: Bioinformatics 11-11-2011, 08:25 AM
Replies: 2
Views: 1,897
Posted By damiankao
Tophat first maps reads to get coverage islands...

Tophat first maps reads to get coverage islands and produce a potential junction database. It then maps against these potential junctions. Then to find smaller exons, it does the segmentation...
Forum: Bioinformatics 11-11-2011, 08:12 AM
Replies: 17
Views: 7,052
Posted By damiankao
There are a lot more resources and tools for perl...

There are a lot more resources and tools for perl than python. But I don't think there is anything inherently special about perl that makes it easier to develop tools or tailor code your own...
Forum: Bioinformatics 11-11-2011, 02:55 AM
Replies: 19
Views: 8,013
Posted By damiankao
I find doing a reference assembly to be...

I find doing a reference assembly to be satisfactory for confirming annotations or maybe extending previous annotations, but not really great for a completely new reference assembly. It might just be...
Forum: Bioinformatics 11-10-2011, 10:08 AM
Replies: 19
Views: 8,013
Posted By damiankao
I've been mainly working with ABI data. If you...

I've been mainly working with ABI data. If you want to do a de novo transcriptome assembly, I would not recommend SOLiD reads, even if they are pair-end.
Forum: Bioinformatics 11-04-2011, 07:53 AM
Replies: 17
Views: 7,052
Posted By damiankao
You can probably do most of it with R. I...

You can probably do most of it with R. I personally prefer python to perl. I think it's easier to learn too.
Forum: Bioinformatics 10-20-2011, 02:42 PM
Replies: 10
Views: 6,651
Posted By damiankao
I understand how the test works. I guess my...

I understand how the test works. I guess my question is does the p-value you obtain from this test useful?

In my example, there are 500 genes out of 10,000 genes that have cell cycle GO term. So...
Forum: Bioinformatics 10-20-2011, 09:13 AM
Replies: 10
Views: 6,651
Posted By damiankao
I guess I am trying to point out that...

I guess I am trying to point out that over-representation analysis gives you significance relative to random chance.

In the case of differential expression, there is no random chance because we...
Forum: Bioinformatics 10-20-2011, 08:28 AM
Replies: 10
Views: 6,651
Posted By damiankao
Thanks. So there really is no point in using an...

Thanks. So there really is no point in using an over-representation analysis in differentially express genes. It doesn't tell you anything in relation to differential expression.
Forum: Bioinformatics 10-20-2011, 05:58 AM
Replies: 10
Views: 6,651
Posted By damiankao
gene ontology over-representation of differentially expressed genes

I am pretty new to the statistical methods used in calculating the probably of over-representation so bear with me. I've been reading this for an intro on this topic:...
Forum: Bioinformatics 10-03-2011, 03:32 AM
Replies: 20
Views: 7,381
Posted By damiankao
It looks like the gtf_to_sam script is not...

It looks like the gtf_to_sam script is not working. Do you have it in your path? Have you tried merging only the cufflinks gtf outputs together? Maybe the USCS gtf is not formatted in a way that...
Forum: Bioinformatics 10-03-2011, 02:47 AM
Replies: 41
Views: 12,495
Posted By damiankao
I agree. I am sure we all understand the...

I agree. I am sure we all understand the drawbacks of using java. If we had a team of developers, then we can worry about what language to use and optimize the **** out of our software. We would also...
Forum: Bioinformatics 09-29-2011, 10:39 AM
Replies: 20
Views: 7,381
Posted By damiankao
Try the solution I posted at: ...

Try the solution I posted at:
http://seqanswers.com/forums/showthread.php?t=11694
Forum: Bioinformatics 09-28-2011, 08:28 AM
Replies: 41
Views: 12,495
Posted By damiankao
Dude, calm down. I think everyone knows java is...

Dude, calm down. I think everyone knows java is not the ideal language to use for creating software. I personally am not a fan of it from a programmer's perspective. But like you said, a cheap labor...
Forum: General 09-28-2011, 03:44 AM
Replies: 1
Views: 1,575
Posted By damiankao
I would try to align your contigs to the closest...

I would try to align your contigs to the closest related species and try to use that to inform your primer design.
Forum: Bioinformatics 09-28-2011, 02:55 AM
Replies: 41
Views: 12,495
Posted By damiankao
It's easy to use and fast to develop....

It's easy to use and fast to develop. Bioinformaticians usually are not hardcore programmers.
Forum: General 09-28-2011, 02:50 AM
Replies: 12
Views: 2,353
Posted By damiankao
People just aren't submitting to the SRA because...

People just aren't submitting to the SRA because its a pain in the ass honestly. Sequences are being generated in such huge volumes and speed, I think it's hard for users to keep up with submissions.
Forum: General 09-28-2011, 02:45 AM
Replies: 3
Views: 988
Posted By damiankao
Read up on genome annotation first. Then...

Read up on genome annotation first.

Then read about SOLiD sequencing.

You have SOLiD sequenced reads. F3 and F5 are the pairs of a mate pair library.

The clc files are for a bioinformatics...
Forum: General 09-28-2011, 02:41 AM
Replies: 5
Views: 5,022
Posted By damiankao
do you just want to merge two fasta files...

do you just want to merge two fasta files together? you can just use the 'cat' linux command for that. So something like this:

cat fastaA.fa fastaB.fa > mergedFasta.fa
Forum: Bioinformatics 09-15-2011, 09:06 AM
Replies: 6
Views: 9,063
Posted By damiankao
To find first common element of two lists in...

To find first common element of two lists in python...


a = [1,2,3,4,5]
b = [6,7,8,9,1,10,12,2,3,4]

intersection = [overlap for overlap in a if overlap in b]

print intersection[0]
Forum: Bioinformatics 06-24-2011, 06:30 AM
Replies: 8
Views: 2,697
Posted By damiankao
I find BioScope to map more reads consistently...

I find BioScope to map more reads consistently (50-60%) and Tophat/Bowtie to map less (30-40%). However, I don't think amount of reads mapped can determine which mapper is "better". The Bowtie manual...
Forum: Bioinformatics 05-31-2011, 09:26 AM
Replies: 21
Views: 13,255
Posted By damiankao
Hi Shurjo, I am by no means an expert on...

Hi Shurjo,

I am by no means an expert on cufflinks or how it works so I can't tell you if that's what you are supposed to get. But I can say the log I got looked similar to yours. Did you get...
Forum: Bioinformatics 05-31-2011, 07:55 AM
Replies: 21
Views: 13,255
Posted By damiankao
I dont't think cuffmerge will merge your fpkms....

I dont't think cuffmerge will merge your fpkms. Its really just for merging the annotations.
Forum: Bioinformatics 05-31-2011, 07:34 AM
Replies: 21
Views: 13,255
Posted By damiankao
Is that exactly how your headers look? My headers...

Is that exactly how your headers look? My headers look something like this:

@HD VN:1.0 SO:coordinate
@SQ SN:scaff000001 LN: 1129481
@SQ SN:scaff000002 LN: 9211615...
Showing results 1 to 25 of 49

 


All times are GMT -8. The time now is 02:21 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO