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Forum: Bioinformatics 09-28-2015, 11:23 AM
Replies: 0
Views: 1,454
Posted By Boel
Question DESeq2 multivariate analysis - retrieving certain stats

Dear All,

I am running a DESeq2 within-subject treatment response analysis. I have RNA seq data on 75 individuals, for most of these I have data before and after treatment (but not all). I also...
Forum: Bioinformatics 02-05-2015, 08:12 AM
Replies: 0
Views: 793
Posted By Boel
cuffmerge not merging?

Hi All,
I have ran:
tophat (w transcriptome index) -> cufflinks (-g & -M) -> cuffmerge -> cuffquant (-M) -> cuffnorm
on a set of >300 samples. In the resulting counts table I have duplicated...
Forum: Bioinformatics 09-05-2014, 05:18 AM
Replies: 16
Views: 7,867
Posted By Boel
Is it recommended to feed 'cuffnorm-counts' to...

Is it recommended to feed 'cuffnorm-counts' to voom/limma?
Forum: RNA Sequencing 04-16-2013, 12:05 AM
Replies: 11
Views: 10,034
Posted By Boel
One possible solution

Dear All,

I am using Cufflinks v2.1.1 and encountered the same error upon running CuffDiff with a mask file and the gencode v15 annotation ("Error: duplicate GFF ID 'ENST00000389680.2'...
Forum: Epigenetics 04-02-2012, 06:44 AM
Replies: 3
Views: 3,594
Posted By Boel
Well, there are the ChIP-seq standards from...

Well, there are the ChIP-seq standards from encode:
http://encodeproject.org/ENCODE/protocols/dataStandards/ChIP_DNase_FAIRE_DNAme_v2_2011.pdf
Forum: Bioinformatics 01-18-2012, 09:00 AM
Replies: 32
Views: 15,771
Posted By Boel
I don't understand what the purpose or effect of...

I don't understand what the purpose or effect of this manipulation would be, could someone please explain? Also, is this still necessary in the latest release of pindel? I have overlapping paired end...
Forum: Epigenetics 12-15-2011, 03:15 PM
Replies: 7
Views: 4,779
Posted By Boel
Haha.. OK, good for you. Hope things go smooth...

Haha.. OK, good for you. Hope things go smooth with the manuscript.
Forum: Epigenetics 12-15-2011, 02:41 PM
Replies: 7
Views: 4,779
Posted By Boel
jwfoley, I have some data coming in which were...

jwfoley,
I have some data coming in which were produced in a very similar setting. How did you end up analyzing your data? Do you have any references for where similar comparisons have been made? ...
Forum: Bioinformatics 11-16-2011, 07:58 AM
Replies: 14
Views: 8,966
Posted By Boel
Glad you solved it! And to answer an earlier...

Glad you solved it!
And to answer an earlier question: I also use much of the data from the Broad resource bundle.
Forum: Bioinformatics 11-16-2011, 07:25 AM
Replies: 6
Views: 2,204
Posted By Boel
I am unable to find any information about a tool...

I am unable to find any information about a tool called oncatator, so I am afraid I can not help you.
Forum: Bioinformatics 11-16-2011, 07:22 AM
Replies: 14
Views: 8,966
Posted By Boel
Hi Elliott, I am not sure what is going...

Hi Elliott,


I am not sure what is going on, but the error might indicate that none of the known variants (hapmap, 1000g or dbsnp) are present in your VCF file. Could that be the case?
Forum: Bioinformatics 11-15-2011, 07:37 AM
Replies: 6
Views: 22,748
Posted By Boel
According to samtools help...

According to samtools help (https://sourceforge.net/mailarchive/message.php?msg_id=27235061) (which includes picard):
"For Illumina paired-end data, the inferred insert size would be the difference...
Forum: Bioinformatics 11-15-2011, 06:49 AM
Replies: 6
Views: 2,204
Posted By Boel
Hi Jane, I'm using SnpEff...

Hi Jane,

I'm using SnpEff (http://snpeff.sourceforge.net/) which is fast and seems to work well. There are other tools as well, such as ANNOVAR and others.
Forum: Bioinformatics 11-15-2011, 06:47 AM
Replies: 14
Views: 8,966
Posted By Boel
Hey reeso123, Could you give us the command...

Hey reeso123,

Could you give us the command used in GATK to produce the given error?

It might be that HaplotypeScore is not part of the default annotation, hence you need to specify in the...
Forum: Bioinformatics 11-15-2011, 06:34 AM
Replies: 6
Views: 22,748
Posted By Boel
Insert size != Fragment size?

Hi All,

This is a very simple question, or should be, but there seems to be some confusion out there.

My understanding is that insert size is the number of bases between paired end reads...
Forum: Bioinformatics 11-03-2011, 10:48 AM
Replies: 5
Views: 3,917
Posted By Boel
I am correct in assuming that using bfast in the...

I am correct in assuming that using bfast in the way I have does create a bias?

Further, when looking at my reads in IGV most (70%) have a insert size that is positive, while my correct mean...
Forum: Bioinformatics 10-31-2011, 03:07 PM
Replies: 5
Views: 3,917
Posted By Boel
Thanks. I started with qseq files, converted...

Thanks.

I started with qseq files, converted them with the ill2fastq.pl and then aligned with bfast (bfast+bwa-0.6.5). Did not use the -k option.

Not sure that this does create a bias, thats...
Forum: Bioinformatics 10-31-2011, 07:52 AM
Replies: 5
Views: 3,917
Posted By Boel
BFAST + GATK -> strand bias?

Hi All,

I have HiSeq exome data, 75 b paired end. I've used bfast to align, which, if I am not mistaking, converts one end to its complement so that both members of a pair are attributed to the...
Forum: Epigenetics 05-09-2011, 11:46 AM
Replies: 2
Views: 2,386
Posted By Boel
Experience with ChIA-PET?

Hi All,

We are looking into ChIA-PET, a tool to look at genome wide chromatin interaction analysis. So far all publications seems to be from the group developing the procedure (PMID: 20181287...
Forum: Bioinformatics 02-22-2011, 12:14 PM
Replies: 1
Views: 3,753
Posted By Boel
HTSeq installation: error: command 'c++' failed with exit status 1

Hi All,

I'm trying to install HTseq-0.4.7p1 on a Mac OS 10.6, with Python 2.6.5, gcc 4.2.1. Below is the full output from "python setup.py install".


$ python setup.py install
running...
Forum: Bioinformatics 02-20-2011, 02:20 PM
Replies: 1
Views: 2,254
Posted By Boel
Hi Pejman, Any progress with the fact that...

Hi Pejman,

Any progress with the fact that so many of the genes with "status = OK" have "Significant = yes"? Kind of seeing the same thing.

Boel
Forum: Bioinformatics 01-14-2011, 08:54 AM
Replies: 1
Views: 1,134
Posted By Boel
Problem solved.

The flag is 4 = unmapped reads.

Unable to delete my first message - sorry about that.
Forum: Bioinformatics 01-14-2011, 07:33 AM
Replies: 1
Views: 1,134
Posted By Boel
Bowtie problem when mapping against short sequences, no positions.

Hi All,

I want to use Bowtie to align reads to exons and junctions. I have created fasta files of the junctions and exons, indexed them and so on. When I run bowtie I end up with aligned reads...
Forum: Bioinformatics 01-04-2011, 06:29 AM
Replies: 2
Views: 2,258
Posted By Boel
Yes there is nothing wrong with my files, and I...

Yes there is nothing wrong with my files, and I was using an up to data version of BEDtools. But! The second file was HUGE, and the command worked when I changed the order of the files. So problems...
Forum: Bioinformatics 12-29-2010, 07:26 AM
Replies: 2
Views: 2,258
Posted By Boel
intersectBed gives empty file

Hi All,

Stumbled on a strange error when running intersectBed (BEDtools) on two samples that I know are partially overlapping. Here are the first five rows of the two files:

File1.gtf, first 5...
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