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Forum: Illumina/Solexa 05-30-2013, 09:44 AM
Replies: 2
Views: 2,834
Posted By clariet
lots of overlapping reads - Pair-end library from Nextera

We have done a couple of run (2X150 and 2X250) of Miseq on bacteria genome sequencing. They all have a high overlapping rate (>80%).

We used Nextera XT for sample prep. I am interested to see any...
Forum: Bioinformatics 09-13-2011, 07:12 AM
Replies: 5
Views: 7,393
Posted By clariet
Yes, you need to create it. A csv file with the...

Yes, you need to create it. A csv file with the following header:

FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator


Sorry, I got it confused with demultiplexing. For bcl...
Forum: Bioinformatics 09-13-2011, 07:10 AM
Replies: 7
Views: 4,044
Posted By clariet
Edge, I am having the same error message. My...

Edge, I am having the same error message. My dataset is 32bp single end. But cuffdiff gave the following message:

> Map Properties:
> Total Map Mass: 8533100.77
> Read Type:...
Forum: Bioinformatics 06-06-2011, 02:30 PM
Replies: 0
Views: 1,740
Posted By clariet
problem running runRNA.pl in CASAVA for RNA-seq data with multiple indexes

I have a RNA-seq dataset run in one lane from Illumina. Each sample has 3 indexes.

I have ran demultiplex.pl and Gerald.pl successful. Now I have export file in each individual index folder. I...
Forum: SOLiD 06-11-2010, 12:24 PM
Replies: 5
Views: 3,664
Posted By clariet
I did it once for a few bacterial samples. I just...

I did it once for a few bacterial samples. I just put multiple .plan file (each plan file has one ini file) in one shell script. It did the job.
Forum: Bioinformatics 05-07-2010, 09:42 AM
Replies: 35
Views: 19,694
Posted By clariet
Thank you. Are you planning to add this sometime...

Thank you. Are you planning to add this sometime soon? My colleague has very good comments on TopHat and I am very much looking forward to using this tool for SOLiD data, which I have access only....
Forum: Bioinformatics 05-07-2010, 09:38 AM
Replies: 18
Views: 11,773
Posted By clariet
I am trying to do the same thing: extract unique...

I am trying to do the same thing: extract unique alignments (single alignments+multiple alignments fulfilling unique criteria).

How exactly could I accomplish this by using SAM view -f (or -F)? I...
Forum: Bioinformatics 05-07-2010, 07:40 AM
Replies: 1
Views: 4,633
Posted By clariet
cufflinks and non-uniquely mapped reads

Cufflinks appear to take not only uniquely mapped reads. I only filtered out low quality mapped reads and ran cufflinks without any problem. But how cufflinks take care of those reads mapped to...
Forum: Bioinformatics 05-07-2010, 07:15 AM
Replies: 35
Views: 19,694
Posted By clariet
Hi, Cole_Trapnell Does current version of...

Hi, Cole_Trapnell

Does current version of Tophat support SOLiD data? Thanks

Clariet
Forum: Bioinformatics 05-03-2010, 10:38 AM
Replies: 2
Views: 2,977
Posted By clariet
Thanks very much for the clarification. I was...

Thanks very much for the clarification. I was trying to detect any splicing difference between 2 samples. That's why I need the exon-level expression. Do you have any suggestions on this?
Forum: Bioinformatics 05-03-2010, 09:52 AM
Replies: 2
Views: 2,977
Posted By clariet
help on Cufflinks output: individual exon have same FPKM

I have run cufflinks for a RNA-seq dataset (SOLiD). As far as I understand, the gtf output file contains the expression level for individual exons. But why all exons from the same gene in my file all...
Forum: Bioinformatics 04-28-2010, 06:31 AM
Replies: 33
Views: 10,613
Posted By clariet
Thank you very much for the reply. I was...

Thank you very much for the reply. I was referring to the 5th column. It IS the mapping quality according to SAM manual. But I guess this mapping quality must be correlated with alignment score for...
Forum: Bioinformatics 04-27-2010, 11:32 AM
Replies: 33
Views: 10,613
Posted By clariet
From the lines below, the score of these...

From the lines below, the score of these alignment are all the same: 255. But from my bioscope output, most of the alignment has less than 10 score. Should I filter out these alignments?


[...
Forum: Bioinformatics 04-26-2010, 11:40 AM
Replies: 14
Views: 6,334
Posted By clariet
Tophat for colorspace reads?

Does current version of Tophat support colorspace reads? I know bowtie does.
Forum: Bioinformatics 04-12-2010, 06:05 AM
Replies: 1
Views: 1,578
Posted By clariet
Please help me out. I am sure many people here...

Please help me out. I am sure many people here has experience with tophat. Could you please point me to the right direction how I could fix it?
Forum: Bioinformatics 04-09-2010, 10:40 AM
Replies: 1
Views: 1,578
Posted By clariet
a tophat running problem

I just installed the latest tophat and bowtie. But I had the following problem when running the test data (also downloaded from tophat web site). The PATH to bowtie and tophat are all right. I am...
Forum: Bioinformatics 04-01-2010, 11:15 AM
Replies: 3
Views: 4,006
Posted By clariet
WIG input file for CEAS (Cis-regulatory Element Annotation System)

I am analyzing a ChIP-seq dataset and want to use CEAS. I have run MACS and got the multiple WIG files (one WIG file for each chromosome and each sample).

But as far as I understand, these WIG...
Forum: Bioinformatics 03-25-2010, 07:55 AM
Replies: 35
Views: 20,974
Posted By clariet
Just saw this post. We were able to use a...

Just saw this post. We were able to use a Whole-transcriptome pipeline of BioScope (1.0.1-42) on a RNA-seq dataset. And a note about its mapping statistics. I confirmed with their specialists that...
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