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Forum: Bioinformatics 03-03-2012, 06:47 AM
Replies: 10
Views: 2,483
Posted By lpn
That works, but subsequent analysis produces...

That works, but subsequent analysis produces strange results.
Forum: Bioinformatics 03-02-2012, 10:24 PM
Replies: 10
Views: 2,483
Posted By lpn
Because tophat doesn't seem to handle well...

Because tophat doesn't seem to handle well Phred+33 (CASAVA 1.8), but works with Phred+64 (CASAVA 1.5+).



Thanks a lot!
Forum: Bioinformatics 03-02-2012, 09:18 AM
Replies: 10
Views: 2,483
Posted By lpn
What about something that I can run in the...

What about something that I can run in the command lane?
Forum: Bioinformatics 03-02-2012, 08:28 AM
Replies: 10
Views: 2,483
Posted By lpn
converting CASAVA 1.8 qual scores

Does anybody have a tested program to convert Illumina CASAVA 1.8 qual scores (Phred+33) to the previous version Illumina 1.5+ (Phred+64)?
Forum: Bioinformatics 03-01-2012, 11:49 AM
Replies: 21
Views: 9,474
Posted By lpn
30-40M pairs. I was running this on the whole...

30-40M pairs. I was running this on the whole transcriptome, but it gave me segmentation fault (shared node on cluster, probably not enough resources), so I decided to run it per chromosome for...
Forum: Bioinformatics 03-01-2012, 11:46 AM
Replies: 21
Views: 9,474
Posted By lpn
Ok, thanks, will look for letters there.

Ok, thanks, will look for letters there.
Forum: Bioinformatics 03-01-2012, 10:59 AM
Replies: 21
Views: 9,474
Posted By lpn
How do I find variants in the pileup file? (sorry...

How do I find variants in the pileup file? (sorry I am new to the SNP business).
Don't have SNP array or gDNA sequencing data for these samples unfortunately.
Forum: Bioinformatics 03-01-2012, 10:56 AM
Replies: 21
Views: 9,474
Posted By lpn
Yes, RNAseq. GAII: 30-40M reads, PE 2x100. ...

Yes, RNAseq. GAII: 30-40M reads, PE 2x100.
There should be at least some SNPs detected with such data.
Forum: Bioinformatics 03-01-2012, 10:36 AM
Replies: 21
Views: 9,474
Posted By lpn
In the pileup file I get things like: chr2 ...

In the pileup file I get things like:
chr2 218208 G 30 ....................,......... +(+++)++++!#+++!+)+++!*****(#(

In the reference the names are like chr2, so they are the...
Forum: Bioinformatics 03-01-2012, 09:29 AM
Replies: 0
Views: 1,024
Posted By lpn
finding SNPs from tophat bam output

I am having trouble with samtools for finding SNPs in bam files produced by tophat:
http://seqanswers.com/forums/showthread.php?p=66400
Any suggestions for other software for finding SNPs from bam...
Forum: Bioinformatics 03-01-2012, 09:23 AM
Replies: 21
Views: 9,474
Posted By lpn
yes, converted that to readable; seems like a...

yes, converted that to readable; seems like a pileup file.
Forum: Bioinformatics 03-01-2012, 09:15 AM
Replies: 21
Views: 9,474
Posted By lpn
Same results Yes, I stopped it; it...

Same results



Yes, I stopped it; it produces something.
Forum: Bioinformatics 03-01-2012, 08:54 AM
Replies: 21
Views: 9,474
Posted By lpn
I looked at the var.raw.bcf; seems too small...

I looked at the var.raw.bcf; seems too small (3k). The raw vcf can't be large either.



How do I look at it? seems like a binary file, but of a good size, several GB.

seems like something...
Forum: Bioinformatics 03-01-2012, 08:35 AM
Replies: 21
Views: 9,474
Posted By lpn
Same result :( Any ideas for finding SNPs...

Same result :(

Any ideas for finding SNPs based on tophat .bam output?
Forum: Bioinformatics 03-01-2012, 07:30 AM
Replies: 21
Views: 9,474
Posted By lpn
problem with samtools and SNP calling

I am trying to do some SNP calling with samtools following this:
http://samtools.sourceforge.net/mpileup.shtml

The issue is that I don't get any SNPs or indels. To check what happens, I modify...
Forum: RNA Sequencing 07-15-2011, 05:13 AM
Replies: 1
Views: 1,784
Posted By lpn
easy way to compute FPKMs from bam files?

Is there an easy way to compute FPKMs from bam files (Tophat output)? I am using cuffdiff to compare 2 samples using an annotation and that gives me the FPKMs for the genes in the annotation, but is...
Forum: Bioinformatics 05-10-2011, 10:31 AM
Replies: 4
Views: 11,986
Posted By lpn
converting bam files to non-normalized read counts

I am new to this business, so I would like to apologize in advance if this is trivial.

I have bam files produced to Tophat and need to run a differential gene expression analysis. I can do that...
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