Forum: Bioinformatics
02-25-2013, 06:48 PM
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Replies: 1
Views: 913
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Forum: Bioinformatics
11-09-2012, 11:58 AM
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Replies: 5
Views: 4,048
Also, just to bring it to the attention, each...
Also, just to bring it to the attention, each read group has to be unique for each library.
If you have same readgroup id (RGID) for two libraries, breakdancer will not be able to perform correctly.
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Forum: Bioinformatics
10-11-2012, 10:49 AM
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Replies: 8
Views: 2,683
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Forum: Bioinformatics
09-28-2012, 12:16 PM
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Replies: 0
Views: 1,401
Cuffdiff Sample v/s replicates FPKM
I ran cuffdiff on two multi-replicate samples. Cuffdiff reports FPKM for each sample as well as FPKM for each replicate.
I was wondering how does it calculate the sample FPKM from its replicate's ...
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Forum: Bioinformatics
09-27-2012, 08:53 PM
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Replies: 21
Views: 4,861
Hi guys,
After reading through the discussion...
Hi guys,
After reading through the discussion above I am realizing that I should also try DESeq. I have two multi-replicate samples and ran cuffdiff on them. Cuffdiff produces a read count files in...
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Forum: Bioinformatics
07-16-2012, 12:38 PM
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Replies: 22
Views: 9,222
Hi catbus,
Did you solve the "segmentation...
Hi catbus,
Did you solve the "segmentation fault" problem with tophat_report?
I tried running the updated version by compiling tophat 2.0.4 as well as using the pre-built binaries... but still...
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Forum: Bioinformatics
07-16-2012, 09:43 AM
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Replies: 22
Views: 14,642
Hi,
When I want to run cutadapt or similar...
Hi,
When I want to run cutadapt or similar adapter trimming program, should I specify both of the Illumina PE adapters for each fastq file? How does program differentiate between the 5' and 3'...
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Forum: Bioinformatics
07-11-2012, 11:10 AM
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Replies: 11
Views: 4,206
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Forum: Bioinformatics
06-27-2012, 12:20 PM
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Replies: 0
Views: 825
bowtie2 genomic data
I was wondering if anyone has run the BowTie2 for genomic data.
My data is paired-end (100-100 bp) and comes from whole genome sequencing.
I am not sure at this stage if I should do end-to-end...
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Forum: Bioinformatics
06-07-2012, 01:46 PM
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Replies: 0
Views: 1,766
read trimming for tophat
Hi,
I am planning to run tophat on my paired-end RNA-Seq data library (75 bp length). Before running tophat, I checked the quality plots. The left end reads look fine but for the right end reads,...
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Forum: De novo discovery
05-21-2012, 10:43 AM
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Replies: 3
Views: 4,195
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Forum: Bioinformatics
05-16-2012, 11:55 AM
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Replies: 34
Views: 14,104
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Forum: Bioinformatics
05-10-2012, 08:33 PM
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Replies: 34
Views: 14,104
Hi Richard,
Thanks a lot for the info. Works...
Hi Richard,
Thanks a lot for the info. Works perfectly.
Does this program make any assumptions about the input bam file (sorting on bam file). Does it also work if I have multiple alignments for...
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Forum: Bioinformatics
05-10-2012, 01:22 PM
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Replies: 34
Views: 14,104
Hi guys,
I've run into a more complex problem...
Hi guys,
I've run into a more complex problem regarding bam to fastq conversion. Somehow my bam files have some unpaired reads mixed with the paired-end reads. I was running Picard but that seems to...
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Forum: Bioinformatics
05-08-2012, 10:29 AM
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Replies: 10
Views: 3,356
Thank GenoMax..
for some reason I can't find...
Thank GenoMax..
for some reason I can't find libboost_thread.so.1.48.0 on my system. My boost installation was successful though. I noticed that /my_boost_install_dir/lib is empty. Is this the...
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Forum: Bioinformatics
05-07-2012, 01:47 PM
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Replies: 10
Views: 3,356
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Forum: Bioinformatics
05-07-2012, 12:23 PM
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Replies: 10
Views: 3,356
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Forum: Bioinformatics
05-07-2012, 10:50 AM
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Replies: 10
Views: 3,356
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Forum: Bioinformatics
05-07-2012, 10:06 AM
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Replies: 10
Views: 3,356
Hi Kopi-o,
Did you figure out the installation...
Hi Kopi-o,
Did you figure out the installation problem yet? I am having another problem with the Eigen libray. I downloaded and copied the eigen-eigen-b23437e61a07/Eigen to a directory in my PATH...
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Forum: RNA Sequencing
04-30-2012, 04:58 PM
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Replies: 5
Views: 2,412
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Forum: RNA Sequencing
04-30-2012, 04:17 PM
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Replies: 5
Views: 2,412
That's a good idea. I thought of that as well....
That's a good idea. I thought of that as well. Actually in the end I also need the expression of each transcript. And after merging assemblies, in order to estimate the expression, I'll need to use...
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Forum: RNA Sequencing
04-30-2012, 12:28 PM
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Replies: 5
Views: 2,412
Merge from multiple libraries + tophat + cufflinks
Hi,
I have two paired-end sequencing RNA-Seq libraries. Both of them are from the same sample but prepared using different insert lengths. I've run tophat on both of them separately. Now I want to...
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Forum: Bioinformatics
04-25-2012, 10:00 PM
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Replies: 11
Views: 17,732
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Forum: Bioinformatics
04-25-2012, 09:59 PM
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Replies: 0
Views: 1,816
Picard SamToFastq is prior sort needed?
Hi,
I am trying to extract paired-end fastq files from a BAM file using Picard's SamToFastq. I was wondering if I need to sort my BAM file on query name before runnign SamtoFastq?
Thanks.
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Forum: Bioinformatics
04-19-2012, 12:38 PM
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Replies: 9
Views: 6,401
SVDetect v/s BreakDancer
Hi,
Has anyone had any experience with SVDetect and BreakDancer? I need some thoughts on their comparison in terms of performance and detection accuracy. I am mainly interested in detecting large...
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