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Forum: Illumina/Solexa 08-29-2012, 01:43 PM
Replies: 2
Views: 4,042
Posted By jujubix
Excerpt from "Summarizing and correcting the GC...

Excerpt from "Summarizing and correcting the GC content bias in high-throughput sequencing" by Benjamini and Speed (2012), which gives some suggestions and citations:



The full paper with...
Forum: Bioinformatics 08-29-2012, 01:27 PM
Replies: 2
Views: 1,058
Posted By jujubix
Without seeing the files or knowing how IGV-tools...

Without seeing the files or knowing how IGV-tools count works, this is purely a guess, but could it be omitting intervals with 0 coverage, which a variableStep .wig file can do? I recall...
Forum: Bioinformatics 08-29-2012, 01:13 PM
Replies: 2
Views: 1,584
Posted By jujubix
I briefly did some work determining CNV events in...

I briefly did some work determining CNV events in matched tumour/normal pairs, from my experience, the difference in coverage between libraries can be corrected for by normalizing the read counts.
...
Forum: Bioinformatics 07-20-2012, 09:34 AM
Replies: 1
Views: 929
Posted By jujubix
Try emailing the authors?

Try emailing the authors?
Forum: Bioinformatics 07-19-2012, 03:59 PM
Replies: 3
Views: 2,381
Posted By jujubix
4 in binary is 100, so '-f 4' will filter for any...

4 in binary is 100, so '-f 4' will filter for any reads with the 3rd bit set to 1
141 in binary is 10001101, whose 3rd bit *is* set to 1, so seeing it is the expected behaviour

For more info on...
Forum: Bioinformatics 07-19-2012, 03:44 PM
Replies: 2
Views: 2,132
Posted By jujubix
I would recommend using the --cluster option in...

I would recommend using the --cluster option in USEARCH (http://www.drive5.com/usearch/). It's freely available for academic use.
Forum: Bioinformatics 07-16-2012, 12:12 PM
Replies: 2
Views: 1,337
Posted By jujubix
You could try using SAMtools...

You could try using SAMtools (http://samtools.sourceforge.net/) to generate pileup (http://samtools.sourceforge.net/pileup.shtml) output, from which you can use Unix cut...
Forum: Bioinformatics 07-16-2012, 11:39 AM
Replies: 1
Views: 1,408
Posted By jujubix
Are you considering the possibility of...

Are you considering the possibility of differences in transcript modification? (i.e. RNA editing (http://en.wikipedia.org/wiki/RNA_editing)) These could explain changes in the protein without any...
Forum: RNA Sequencing 05-09-2012, 07:14 PM
Replies: 7
Views: 6,339
Posted By jujubix
No, I do not know. Although the manual...

No, I do not know. Although the manual (http://bio-bwa.sourceforge.net/bwa.shtml) probably says no?
Forum: RNA Sequencing 05-09-2012, 03:19 PM
Replies: 7
Views: 6,339
Posted By jujubix
Maybe TopHat (http://tophat.cbcb.umd.edu/) with...

Maybe TopHat (http://tophat.cbcb.umd.edu/) with the '--library-type' option which will treat the reads in a strand specific manner as described in the manual (http://tophat.cbcb.umd.edu/manual.html)?
Forum: Bioinformatics 05-03-2012, 02:40 PM
Replies: 7
Views: 3,018
Posted By jujubix
Yeah, at this point building a common reference...

Yeah, at this point building a common reference via assembly is looking mighty tempting. This of course, assuming cerebralrust has the major computer power to run everything ;)
Forum: Bioinformatics 05-03-2012, 02:21 PM
Replies: 7
Views: 3,018
Posted By jujubix
De novo assembly, as sdriscoll mentioned, is the...

De novo assembly, as sdriscoll mentioned, is the typical solution when no decent reference genome exists.

Given that you're dealing with gene expression, I assume you have transcriptome reads, in...
Forum: Bioinformatics 05-01-2012, 01:50 PM
Replies: 2
Views: 2,070
Posted By jujubix
modENCODE Drosophila (http://www.modencode.org/)...

modENCODE Drosophila (http://www.modencode.org/) has several strand-specific RNA-seq libraries, although I'm not sure they have corresponding RT-PCR data...

12 strand-specific embryonic total-RNA...
Forum: Bioinformatics 05-01-2012, 01:41 PM
Replies: 8
Views: 3,135
Posted By jujubix
deFuse maybe? ...

deFuse maybe?

http://compbio.bccrc.ca/software/defuse/

It was tested on Illumina GAII paired end tumour data, which seems to fit your needs?
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