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Forum: Bioinformatics 03-03-2015, 02:23 PM
Replies: 2
Views: 1,517
Posted By bioinfosm
In some cases, there might be overlapping primers...

In some cases, there might be overlapping primers and amplicons where simply ignoring the areas wouldnt be a good idea. In those cases, trimming is still important as the variant allele frequencies...
Forum: Bioinformatics 06-05-2014, 12:50 PM
Replies: 3
Views: 1,848
Posted By bioinfosm
i think you should change the query to aligner...

i think you should change the query to aligner for multiply mapped reads!
most aligners you mention have different options to select multiply mapped reads, so it might end up being multiple options...
Forum: Bioinformatics 02-07-2013, 10:42 AM
Replies: 15
Views: 8,291
Posted By bioinfosm
Hey, Do you know why GATK does it on...

Hey,

Do you know why GATK does it on dinucleotides and not mono- or tri- nucleotides.. are the reasons computation or the reagent chemistry, etc?

thanks!
Forum: Academic/Non-Profit Jobs 07-23-2012, 01:50 PM
Replies: 1
Views: 1,675
Posted By bioinfosm
We have more openings for bioinformatics,...

We have more openings for bioinformatics, especially for NGS analysis
http://www.mayo-clinic-jobs.com/job/Rochester-Informatics-Specialist-Job-MN-55901/1688902/

And the updated link for the more...
Forum: General 07-05-2012, 07:06 AM
Replies: 3
Views: 1,737
Posted By bioinfosm
nevermind, i think this is the one =...

nevermind, i think this is the one = http://www.flexgen.nl/index.php?cat=tools&page=flexcalc
Forum: General 07-05-2012, 07:03 AM
Replies: 3
Views: 1,737
Posted By bioinfosm
Did you actually launch it? is the cost...

Did you actually launch it? is the cost calculator available for use?
Forum: Events / Conferences 06-12-2012, 01:55 PM
Replies: 0
Views: 934
Posted By bioinfosm
Call for Abstracts Individualizing Medicine 2012 by Mayo Clinic

Abstract submission closes Friday, June 15, for Individualizing Medicine 2012: Transforming Patient Care with Genomics.

We’re looking for a diversity of ideas and realize that individualized...
Forum: Bioinformatics 05-31-2012, 12:33 PM
Replies: 2
Views: 899
Posted By bioinfosm
If it is so homologus, you are bound to see...

If it is so homologus, you are bound to see mis-alignment. It might be a good idea to check out mappability features for your genes of interest. Perhaps a longer read application would be more suited...
Forum: Bioinformatics 05-31-2012, 12:25 PM
Replies: 3
Views: 1,058
Posted By bioinfosm
ohh well, here is another option, though am not...

ohh well, here is another option, though am not sure if variants includes indels
http://seqanswers.com/forums/showthread.php?t=18541
Forum: Bioinformatics 05-31-2012, 12:23 PM
Replies: 3
Views: 1,058
Posted By bioinfosm
I agree .. you would need to parse the pileup...

I agree .. you would need to parse the pileup file and then use your own thresholds. Perhaps use the simple common filters and start with that indel list.

For annotation, seattleSEQ...
Forum: Bioinformatics 05-31-2012, 12:04 PM
Replies: 13
Views: 4,169
Posted By bioinfosm
Is it possible for you to share the final...

Is it possible for you to share the final solution, and where the ancestral allele sequence can be obtained from?

I know Petr provided most of the snippets, but if you can summarize the working...
Forum: General 04-16-2012, 02:24 PM
Replies: 1
Views: 4,388
Posted By bioinfosm
I just posted this on biostar ...

I just posted this on biostar

http://www.biostars.org/post/show/17335/where-to-find-a-good-estimate-of-the-background-mutation-rate-in-rattus-norvegicus/#42809

This paper...
Forum: Personalized Genomics 04-10-2012, 08:08 PM
Replies: 8
Views: 4,880
Posted By bioinfosm
SmartPhone APP for personalized genome

Just noticed that EdgeBio released their iTunes app today with twitter, facebook and social features .. any others already out there?

I remember Illumina's Bentley talking about the iPhone app,...
Forum: General 04-10-2012, 07:59 PM
Replies: 23
Views: 106,668
Posted By bioinfosm
hey thats cool! congrats!!

hey thats cool! congrats!!
Forum: Bioinformatics 04-10-2012, 07:48 PM
Replies: 17
Views: 7,379
Posted By bioinfosm
perhaps you can use the variant calls from this...

perhaps you can use the variant calls from this sample along with the reference sequence to sort of come up with 'the' sequence for this individual
Forum: Bioinformatics 04-10-2012, 07:46 PM
Replies: 4
Views: 840
Posted By bioinfosm
how does this compare to cutadapt tool?

how does this compare to cutadapt tool?
Forum: Bioinformatics 04-10-2012, 07:44 PM
Replies: 9
Views: 6,899
Posted By bioinfosm
thats interesting. Why would you need that...

thats interesting. Why would you need that correlation? why not just use a statistical model, like the ones in useq or macs, and when you input the replicates as case and control, obtain not many...
Forum: Bioinformatics 04-10-2012, 07:42 PM
Replies: 9
Views: 5,447
Posted By bioinfosm
seems you need to do some more reading! Here is...

seems you need to do some more reading!
Here is the mRNA-seq analysis guide = http://seqanswers.com/wiki/How-to/RNASeq_analysis
you would need to do the alignments on the entire genome, but then...
Forum: Bioinformatics 04-10-2012, 07:38 PM
Replies: 9
Views: 1,499
Posted By bioinfosm
or you can try splitting the bam file by...

or you can try splitting the bam file by chromosome and then calling SNP on them separately.. you could also try starting from the fastq or qseq files, run alignment using something like bwa and then...
Forum: Bioinformatics 04-10-2012, 07:29 PM
Replies: 3
Views: 2,678
Posted By bioinfosm
This can be a good starting point for you:...

This can be a good starting point for you: http://seqanswers.com/wiki/How-to/RNASeq_analysis

Do start with around 30 - 50 million reads to do useful analysis
Forum: Academic/Non-Profit Jobs 03-09-2012, 02:25 PM
Replies: 1
Views: 1,675
Posted By bioinfosm
Multiple Bioinformatics job-openings at Mayo Clinic

Looking for Bioinformatics personnel. Please refer to individual job descriptions for details

http://www.mayo-clinic-jobs.com/job/Rochester-Informatics-Specialist-Job-MN-55901/1688902/...
Forum: Academic/Non-Profit Jobs 12-16-2011, 02:27 PM
Replies: 0
Views: 1,617
Posted By bioinfosm
Informatics Specialist (IT) @ Mayo Clinic

http://www.mayo-clinic-jobs.com/job/Rochester-Informatics-Specialist-Job-MN-55901/1584922/?utm_source=J2WRSS&utm_medium=rss&utm_campaign=J2W_RSS
Forum: Academic/Non-Profit Jobs 11-17-2011, 02:32 PM
Replies: 0
Views: 1,325
Posted By bioinfosm
Informatics Specialists @ Mayo Clinic

Check out the original job posting here:
http://www.mayo-clinic-jobs.com/job/Rochester-Informatics-Specialist-Job-MN-55901/1530977/

Next-gen sequencing, systems biology or data integration...
Forum: Site Feedback/Suggestions 11-10-2011, 02:48 PM
Replies: 430
Views: 47,342
Posted By bioinfosm
got really tied up for the past couple months,...

got really tied up for the past couple months, but this is very interesting, and can look to contribute.

I will start with scrolling through the thread, but feel free to PM me with any specifics..
Forum: Events / Conferences 09-13-2011, 12:12 PM
Replies: 1
Views: 1,639
Posted By bioinfosm
Beyond The Genome 2011 - Washington DC

http://www.beyond-the-genome.com/program.html

Any seq'sters attending this one?
Showing results 1 to 25 of 482

 


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