SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 16 of 16
Search took 0.00 seconds.
Search: Posts Made By: prm36
Forum: Bioinformatics 09-14-2012, 01:33 AM
Replies: 5
Views: 3,043
Posted By prm36
Same place

Same place
Forum: Bioinformatics 02-16-2012, 03:03 AM
Replies: 5
Views: 3,043
Posted By prm36
You can request the software from Roche here: ...

You can request the software from Roche here:
http://my454.com/contact-us/software-request.asp
Forum: Bioinformatics 02-10-2012, 08:24 AM
Replies: 15
Views: 4,241
Posted By prm36
What depth of coverage are you averaging for you...

What depth of coverage are you averaging for you sample?
You have specified a maximum cut off of 200 for your variant calling, is it possible that the site you are looking at has coverage >200?
Forum: Bioinformatics 11-23-2011, 05:07 AM
Replies: 6
Views: 2,814
Posted By prm36
Oops, forgot to include link! ...

Oops,
forgot to include link!

http://www.ncbi.nlm.nih.gov/pubmed/21864619
Forum: Bioinformatics 11-23-2011, 04:44 AM
Replies: 6
Views: 2,814
Posted By prm36
Shameless self promotion. Paper describing...

Shameless self promotion. Paper describing application of SVMs for the prediction of putative vaccine candidates from bacterial genome sequence.

Paul
Forum: Bioinformatics 10-11-2011, 07:52 AM
Replies: 3
Views: 2,061
Posted By prm36
I just checked my lab book for my notes for when...

I just checked my lab book for my notes for when I found myself having the same problem.

"""
Reads with multiple mismatches are mapping.
If one read of a pair maps, SW algorithm in bwa will map...
Forum: Bioinformatics 10-11-2011, 07:44 AM
Replies: 3
Views: 2,061
Posted By prm36
I find that by running bwa sampe with the -s...

I find that by running bwa sampe with the -s option, the second read of the pair does not get mapped, and thus resolves this issue.
Forum: Bioinformatics 10-07-2011, 03:05 AM
Replies: 6
Views: 5,482
Posted By prm36
Hi, did you ever find a way to solve this?

Hi,
did you ever find a way to solve this?
Forum: Bioinformatics 09-21-2011, 07:23 AM
Replies: 2
Views: 2,281
Posted By prm36
http://wiki.g2.bx.psu.edu/Learn

http://wiki.g2.bx.psu.edu/Learn
Forum: De novo discovery 08-30-2011, 12:33 AM
Replies: 3
Views: 2,323
Posted By prm36
We take 2x coverage for SNP calling in our lab. ...

We take 2x coverage for SNP calling in our lab.

Ventner's genome was done to 7.5x (http://www.nature.com/nrg/journal/v11/n1/pdf/nrg2626.pdf)

Cheers

Paul
Forum: Bioinformatics 07-14-2011, 08:11 AM
Replies: 3
Views: 2,131
Posted By prm36
Thank you!!

Thank you!!
Forum: Bioinformatics 07-14-2011, 08:10 AM
Replies: 3
Views: 2,131
Posted By prm36
Thank you!

Thank you!
Forum: Bioinformatics 07-14-2011, 08:07 AM
Replies: 3
Views: 2,131
Posted By prm36
consensus from mpileup

Hi,

I am trying to call the consensus sequence from an mpileup file using samtools (specifically the vcf2fq command).

The consensus fastq file is produced, and looks correct, but during the...
Forum: Bioinformatics 02-08-2011, 08:57 AM
Replies: 0
Views: 1,756
Posted By prm36
Coverage required to call SNPs from 454 data?

Hi,

I've mostly worked on Illumina data and have all my SNP calling scripts tuned to data from that platform.

I have recently received some 454 data and am wondering what is an appropriate...
Forum: Bioinformatics 04-15-2010, 07:29 AM
Replies: 0
Views: 1,267
Posted By prm36
MAQ paired ends

Hi all, I'm running maq.pl easyrun to assemble bacterial sequences. However I am not getting the unmapped reads dumped to a file as I do when assembling single end reads.

Is it possible to dump...
Forum: Bioinformatics 03-12-2010, 09:12 AM
Replies: 0
Views: 1,213
Posted By prm36
maq map problem

Hi,

I am attempting to assemble SOLEXA reads from a bacterial genome.
I have been able to assemble the reads from the raw fastq file.
I have filtered and trimmed the fastq file to remove low...
Showing results 1 to 16 of 16

 


All times are GMT -8. The time now is 01:55 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO