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Forum: Metagenomics 07-21-2016, 10:00 AM
Replies: 0
Views: 1,113
Posted By MQ-BCBB
Post New metagenomics analysis platform: Nephele

I think many of you could benefit from using this new tool for Metagenomics data analysis (16S, ITS, WGS) created in NIAID/NIH.
Misner I, Dommer J, Ezeji S et al. Nephele: A cloud-based scientific...
Forum: Bioinformatics 02-09-2016, 09:46 AM
Replies: 0
Views: 1,273
Posted By MQ-BCBB
Lightbulb Nephele:cloud-based microbiome analysis tool for 16S and WGS data

NIAID has announced the public launch of Nephele for your microbiome analysis needs.
Why Use Nephele? Nephele is designed to be a no-hassle, powerful and easy-to-use tool to support your research. ...
Forum: Metagenomics 02-09-2016, 09:14 AM
Replies: 13
Views: 3,829
Posted By MQ-BCBB
You could also make a biom file in mothur then...

You could also make a biom file in mothur then use qiime scripts for visualization. I would recommend you try Nephele <https://nephele.niaid.nih.gov> which has easy to use pipelines based on mothur...
Forum: Bioinformatics 04-15-2013, 08:50 AM
Replies: 11
Views: 2,674
Posted By MQ-BCBB
Since no one has mentioned SnpSIFT, I should way...

Since no one has mentioned SnpSIFT, I should way that it works very well for this
http://snpeff.sourceforge.net/SnpSift.html#casecontrol
Forum: Bioinformatics 04-25-2012, 11:39 AM
Replies: 36
Views: 12,969
Posted By MQ-BCBB
With version GenomeAnalysisTK-1.5-32, I still...

With version GenomeAnalysisTK-1.5-32, I still have the same problem. Using the -rf BadCigar allows the UnifiedGenotyper analysis to proceed.
Forum: Bioinformatics 02-09-2012, 12:47 PM
Replies: 8
Views: 4,869
Posted By MQ-BCBB
error

Hello Zam, I am working with Martine in trying to run cortex. I ran the following line and received the error below:

command:
cortex_var_31_c1 --pe_list PyN67C_R1.fastq,PyN67C_R2.fastq --format...
Forum: Bioinformatics 02-02-2012, 12:46 PM
Replies: 16
Views: 7,346
Posted By MQ-BCBB
Hello, I just had the same problem but found...

Hello,

I just had the same problem but found that the solution is the following:

Add name and file type after the -knownSites argument. If you file is in vcf format, use the following.
...
Forum: Bioinformatics 10-20-2011, 04:16 PM
Replies: 138
Views: 59,434
Posted By MQ-BCBB
Great resource!!! Just a few comments: In...

Great resource!!!
Just a few comments:
In the picard/MarkDuplicates.jar, the option 'CREATE_INDEX=true' should be added.
With respect to adding read group information, instead of using the...
Forum: Bioinformatics 04-14-2011, 10:24 AM
Replies: 15
Views: 8,011
Posted By MQ-BCBB
@Tonybolger Yes, such tool would be nice to...

@Tonybolger
Yes, such tool would be nice to have! Thanks in advance!
Forum: Bioinformatics 10-28-2010, 10:08 AM
Replies: 21
Views: 15,432
Posted By MQ-BCBB
Thanks, thanks for the -Q 33 tip. So helpful!

Thanks, thanks for the -Q 33 tip. So helpful!
Forum: Bioinformatics 08-05-2010, 05:30 AM
Replies: 9
Views: 8,648
Posted By MQ-BCBB
Hello, Did you ever found the cause of the...

Hello,
Did you ever found the cause of the error?
Thank you,
Mariam.
Forum: 454 Pyrosequencing 05-21-2010, 08:58 AM
Replies: 7
Views: 4,817
Posted By MQ-BCBB
Asifrim, The bank2contig wtih the -S option...

Asifrim,

The bank2contig wtih the -S option doesn't give a SAM format. According to the documentation online, conversion to SAM should be using the -s option but as of version 2.0.8 that is not...
Forum: Introductions 04-05-2010, 11:21 AM
Replies: 83
Views: 76,650
Posted By MQ-BCBB
loved your post

:D I felt exactly like that not too long ago. And yes, I still remember the great feeling when I successfully loaded my data into IGV.
Forum: Literature Watch 02-11-2010, 06:46 AM
Replies: 0
Views: 1,328
Posted By MQ-BCBB
Nature Feb11: Ancient human genome sequence of an extinct Palaeo-Eskimo

Abstract:
We report here the genome sequence of an ancient human. Obtained from ~4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to...
Forum: Bioinformatics 11-16-2009, 07:00 AM
Replies: 4
Views: 5,756
Posted By MQ-BCBB
See the answer in the following post describing...

See the answer in the following post describing the use of Galaxy.

http://seqanswers.com/forums/showthread.php?t=2711&highlight=blat+output
Forum: Bioinformatics 11-16-2009, 06:48 AM
Replies: 11
Views: 12,997
Posted By MQ-BCBB
Thanks for your reply. I haven't tried it but I...

Thanks for your reply. I haven't tried it but I will. I also found convenient to get to a sam output which could be sorted and indexed with the IGV tools and then displayed in the browser.
Forum: Literature Watch 10-21-2009, 04:44 PM
Replies: 10
Views: 4,724
Posted By MQ-BCBB
Thank you! Shortly after I posted, I figure it...

Thank you!
Shortly after I posted, I figure it out. The program worked fine. In fact, when I used ssaha2+samtools pileup or BLAT+Varscan, I obtained similar results in the number of SNPs that were...
Forum: Bioinformatics 09-30-2009, 03:22 PM
Replies: 11
Views: 12,997
Posted By MQ-BCBB
how to convert BLAT output (pslx or maf) to gff, sam, wig to load in browser

I was able to view BLAT output (psl format) in the IGB (igb.bioviz.org) but would like to be able to use the BROAD IGV instead which doesn't recognize any of the BLAT outputs.

Is there a way to...
Forum: Bioinformatics 09-24-2009, 01:08 PM
Replies: 30
Views: 17,348
Posted By MQ-BCBB
kmcarr, I am very thankful for the script. ...

kmcarr,

I am very thankful for the script. It worked for me too! :)
Forum: Literature Watch 09-23-2009, 12:53 PM
Replies: 10
Views: 4,724
Posted By MQ-BCBB
Hello, The program looked very useful from the...

Hello,
The program looked very useful from the description in the paper. I tried installing in Mac and Linux but it gave me errors (needed Math::Pari). I googled it and found some information but...
Forum: Bioinformatics 09-08-2009, 11:24 AM
Replies: 5
Views: 2,231
Posted By MQ-BCBB
JimC, I am having a similar problem, did you...

JimC, I am having a similar problem, did you figure out why you were loosing most reads?
Thanks!
Forum: Bioinformatics 08-13-2009, 08:37 AM
Replies: 3
Views: 1,409
Posted By MQ-BCBB
Unix basics

Hello,

Check this link that someone forwarded to me recently for an introduction to Unix and Perl for biologists. It is very well written and include other course materials. It is based on a...
Forum: Bioinformatics 06-09-2009, 07:52 PM
Replies: 26
Views: 7,648
Posted By MQ-BCBB
I was able to download and map 454 reads

Thank you making this tool available. :) It took much longer than expected; I will then explore results.

MQ
Forum: Bioinformatics 06-09-2009, 12:53 PM
Replies: 26
Views: 7,648
Posted By MQ-BCBB
links not working

Sven, the links are not accessible from my end either. I am curious to try, hope the issue gets resolved.

MQ
Forum: Introductions 05-12-2009, 07:24 AM
Replies: 0
Views: 920
Posted By MQ-BCBB
Hello from Mariam

Hello! Working at BCBB, a bioinformatics group at NIAID/NIH and learning a lot from this forum.:)
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