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Forum: De novo discovery

06-13-2012, 10:20 AM

Replies: 36

The best genome de novo assembly software using hybrid data (Illumina, 454 & Sanger)?

Views: 9,164

Posted By d f

Thanks for the info! I will give it a try. ...

Thanks for the info! I will give it a try.

I already created separate 454/Newbler and Illumina/SGA assemblies, and when I BLAT aligned the shorter Illumina/SGA scaffolds against the longer...

Forum: De novo discovery

06-11-2012, 02:24 PM

Replies: 36

The best genome de novo assembly software using hybrid data (Illumina, 454 & Sanger)?

Views: 9,164

Posted By d f

Hi ians, In your poster, you'd found that...

Hi ians,

In your poster, you'd found that for genomes >10Mb, it is better to pre-assemble the 454 reads, and then combine the 454 pre-assembled fragments with the Illumina reads for the final...

Forum: Bioinformatics

08-03-2011, 01:48 PM

Replies: 2

latest SAM format: did the meanings of read and fragment get swapped?

Views: 890

Posted By d f

latest SAM format: did the meanings of read and fragment get swapped?

In the latest SAM format specification, the meanings of "read" and "fragment" seem to be reversed from what I am accustomed to.

My understanding is that a fragment is the result of breaking a...

Forum: Bioinformatics

04-04-2011, 09:09 AM

Replies: 3

Good annotation editor?

Views: 1,087

Posted By d f

Thanks! I'll look into UGENE. d f

Thanks! I'll look into UGENE.

d f

Forum: Bioinformatics

04-01-2011, 11:51 AM

Replies: 3

Good annotation editor?

Views: 1,087

Posted By d f

Good annotation editor?

I am seeking a good annotation editor. I have genes predicted by ab initio and RNA-seq gene/transcript predictors, but many of the predictions need to be fixed by hand. I am seeking an easy way to...

Forum: Bioinformatics

03-07-2011, 02:57 PM

Replies: 2

IGV: display six-frame (amino-acid) translation of reference genome?

Views: 1,666

Posted By d f

I contacted igv-help [at] broadinstitute.org . I...

I contacted igv-help [at] broadinstitute.org . I got a reply saying that the six-frame translation will be available in the upcoming IGV 2.0 release, which you can access at...

Forum: Bioinformatics

03-03-2011, 10:22 AM

Replies: 2

IGV: display six-frame (amino-acid) translation of reference genome?

Views: 1,666

Posted By d f

IGV: display six-frame (amino-acid) translation of reference genome?

In IGV, is it possible to display the six-frame (amino-acid) translation of the reference genome?

That would be helpful for assessing the accuracy of gene models.

Forum: Bioinformatics

11-10-2010, 11:00 AM

Replies: 4

TopHat closure-search: what does it do?

Views: 1,468

Posted By d f

TopHat closure-search: what does it do?

What does the --closure-search option of TopHat do?

Forum: Bioinformatics

11-09-2010, 11:30 AM

Replies: 0

how does cuffcompare choose which transcript to put in combined.gtf file?

Views: 668

Posted By d f

how does cuffcompare choose which transcript to put in combined.gtf file?

When cuffcompare is run with multiple input gtf files from different sequencing expts, how does it decide which transcript to be the "representative" transcript to list in the combined.gtf file? ...

Forum: Bioinformatics

10-28-2010, 08:45 AM

Replies: 11

Cufflinks' estimated fragment length mean and standard deviation

Views: 2,258

Posted By d f

Thanks, kmcarr! I had a similar problem: The...

Thanks, kmcarr!

I had a similar problem: The fragment length estimated by Cufflinks completely disagreed with that measured by the Agilent High Sensitivity Chip. But, subtracting 119bp from the...

Forum: Bioinformatics

10-19-2010, 10:49 AM

Replies: 11

Cufflinks' estimated fragment length mean and standard deviation

Views: 2,258

Posted By d f

Thanks for the info! I guess my fragments...

Thanks for the info!

I guess my fragments are a lot shorter than what the Agilent High Sensitivity chip predicts/measures. Sigh.

Forum: Bioinformatics

10-18-2010, 01:31 PM

Replies: 11

Cufflinks' estimated fragment length mean and standard deviation

Views: 2,258

Posted By d f

Cufflinks' estimated fragment length mean and standard deviation

I have a question about the Fragment Length Distribution that Cufflinks (v 0.9.0+) estimates, based on paired end read alignments:

Is this the length of the fragment, including the two reads; or...

Forum: Illumina/Solexa

09-28-2010, 09:46 AM

Replies: 4

FastQC "Per Base Sequence Content": systematic deviation at 3' end of reads

Views: 2,434

Posted By d f

Thanks for the advice!!! This is my first...

Thanks for the advice!!!

This is my first time working with Illumina data, and my first time doing RNA-seq, so any and all advice is helpful!

Forum: Illumina/Solexa

09-27-2010, 01:17 PM

Replies: 4

FastQC "Per Base Sequence Content": systematic deviation at 3' end of reads

Views: 2,434

Posted By d f

Thanks much, kmcarr, for the info and for the...

Thanks much, kmcarr, for the info and for the speedy reply!

Out of curiosity, I took the final 32bp from each read, and ran them through FastQC. Indeed, the Overrepresented Sequences are Illumina...

Forum: Illumina/Solexa

09-24-2010, 04:35 PM

Replies: 4

FastQC "Per Base Sequence Content": systematic deviation at 3' end of reads

Views: 2,434

Posted By d f

FastQC "Per Base Sequence Content": systematic deviation at 3' end of reads

I have 101 bp Illumina GA IIx RNA-seq reads that display strange behavior in their FastQC "Per Base Sequence Content". I'm wondering if anyone knows what is causing this, or has seen similar...

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