SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 12 of 12
Search took 0.00 seconds.
Search: Posts Made By: phoss
Forum: Bioinformatics 05-02-2012, 08:51 PM
Replies: 7
Views: 3,017
Posted By phoss
Hi cerebralrust, I was curious if you've...

Hi cerebralrust,

I was curious if you've tried M. truncatula? This a close relative of G. max.
Have you had any luck with genomes off of phytozome?
Forum: RNA Sequencing 04-18-2012, 07:58 AM
Replies: 12
Views: 8,659
Posted By phoss
Hi Himanshu, I personally have not worked with...

Hi Himanshu,
I personally have not worked with M. musculus but I recall a well-known mouse resource to be 'Mouse Genome Informatics' (MGI).
You could use MGI Biomart (under Analysis Tools) to...
Forum: Bioinformatics 04-18-2012, 07:32 AM
Replies: 9
Views: 4,493
Posted By phoss
Hi detq182, Why not delimit your fasta header...

Hi detq182,
Why not delimit your fasta header with a special character such as colon or vertical bar?
For example:
>header | supplemental-info

This way, you can embed many annotations adjacent...
Forum: RNA Sequencing 04-16-2012, 08:49 PM
Replies: 12
Views: 8,659
Posted By phoss
Hi Himanshu, Glad it was helpful. We obtained...

Hi Himanshu,
Glad it was helpful.
We obtained accession-to-EC mappings via biomart. If however such mappings do not exist for your model, you could use uniprot by running uniprot BLAST against your...
Forum: RNA Sequencing 04-16-2012, 06:02 PM
Replies: 12
Views: 8,659
Posted By phoss
Hi Himanshu, We've done similar work ourselves....

Hi Himanshu,
We've done similar work ourselves.
What we did was map each differentially-expressed gene onto their respective Enzyme Commission accession (EC). Doing so was quite helpful because as...
Forum: Bioinformatics 04-08-2012, 08:14 AM
Replies: 4
Views: 2,195
Posted By phoss
Hi henry_by, If I'm not mistaken, EBI has GO...

Hi henry_by,
If I'm not mistaken, EBI has GO annotations embedded in some fasta headers. You may want to look into creating a local blast-instance of these files and locally-blast your predicted...
Forum: Illumina/Solexa 04-07-2012, 06:07 PM
Replies: 16
Views: 7,019
Posted By phoss
Hi kmcarr, What we noticed during some of our...

Hi kmcarr,
What we noticed during some of our multiplex-runs (single-end) was that the sequencing of the actual read was great... high quality scores, several million reads, etc. The indexes on the...
Forum: Illumina/Solexa 04-05-2012, 08:28 AM
Replies: 16
Views: 7,019
Posted By phoss
Hi uattsoancrik, What I had meant to say in my...

Hi uattsoancrik,
What I had meant to say in my prior post was whether you see specific DNA patterns in the indexes which map to 'contaminated' samples.

In response to your question: We had the...
Forum: Illumina/Solexa 04-04-2012, 10:10 PM
Replies: 16
Views: 7,019
Posted By phoss
Hi uattsoancrik, We had a similar problem to...

Hi uattsoancrik,
We had a similar problem to your original post; saw such results with some multiplexed samples on the GAIIx.
Just curious: the contaminated samples you mentioned originally... are...
Forum: Bioinformatics 10-17-2011, 04:43 PM
Replies: 11
Views: 2,579
Posted By phoss
Hi Kashliks, We were all beginners in the world...

Hi Kashliks,
We were all beginners in the world of NGS at some point :)

My 2c: I'd encourage you to see what the goal of NGS is and why it would fit your project goals. Like Simon Anders and...
Forum: Bioinformatics 08-27-2011, 11:47 AM
Replies: 5
Views: 3,966
Posted By phoss
If I'm not mistaken, Blast2GO limits sequences to...

If I'm not mistaken, Blast2GO limits sequences to 10,000bps.
Forum: Illumina/Solexa 08-24-2011, 08:48 PM
Replies: 2
Views: 3,852
Posted By phoss
Hi Angela, We had a similar problem to what you...

Hi Angela,
We had a similar problem to what you outlined (we also ran a multiplexed run on the IIx, several actually). Was the sample concentration in lanes 3 and 6 the same across all other lanes,...
Showing results 1 to 12 of 12

 


All times are GMT -8. The time now is 04:31 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO