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Forum: RNA Sequencing 04-10-2015, 06:33 AM
Replies: 3
Views: 1,228
Posted By shirley0818
Hi GenoMax, I have figured it out by adding...

Hi GenoMax,

I have figured it out by adding -wa -wb option:
bedtools intersect -wa -wb -a A.bed -b B.bed

Many thanks,
Shirley
Forum: RNA Sequencing 04-09-2015, 04:44 PM
Replies: 3
Views: 1,228
Posted By shirley0818
Thanks GenoMax for your quick response. I have...

Thanks GenoMax for your quick response. I have tried "bedtools" as you suggested, but got very strange results: Below are the example files and output.

1. Here is s1.junction.bed file generated by...
Forum: RNA Sequencing 04-09-2015, 08:10 AM
Replies: 3
Views: 1,228
Posted By shirley0818
how to combine junction.bed files with different rows into one table

Hi All,

I am working on ~100 samples for detecting alternative splicing. TopHat generates a junction.bed file for each sample. However, each of these bed files has different number of rows, and...
Forum: RNA Sequencing 01-27-2015, 06:28 PM
Replies: 0
Views: 1,074
Posted By shirley0818
how to visualize a few hundreds RNAseq samples in IGV/GenomeBrowser

Hi All,

I have been using IGV tool to visualize my RNASeq data from a few samples by creating a .tdf file for each sample.

Now I have 100 samples from Group A, and another 100 samples from...
Forum: RNA Sequencing 07-22-2014, 11:47 AM
Replies: 0
Views: 1,682
Posted By shirley0818
compare RNASeq with Exon array data at the gene-level and exon-level

Dear List,

I have 50 RNA samples and each sample has the following expression data:

1. Illumina RNAseq 75bp paired-end data
2. Affymetrix Human Exon 1.0 ST array

My goal is to compare...
Forum: RNA Sequencing 03-26-2014, 06:37 AM
Replies: 6
Views: 1,754
Posted By shirley0818
Thanks MU Core. In our experiments, the...

Thanks MU Core.

In our experiments, the average RNA fragments is about 200-300bp, so the 2x75bp might be better for alternative splicing as Brian suggested. we will definitely not go to 2x100 at...
Forum: RNA Sequencing 03-25-2014, 11:00 AM
Replies: 6
Views: 1,754
Posted By shirley0818
Great. Thank you for your suggestions. Have a...

Great. Thank you for your suggestions. Have a nice day!
Forum: RNA Sequencing 03-25-2014, 10:50 AM
Replies: 6
Views: 1,754
Posted By shirley0818
Thanks Brian for your quick response. We would...

Thanks Brian for your quick response. We would like to differential expression analysis,
alternative splicing, novel transcripts, etc.

But most importantly, in the near future, we will have 2...
Forum: RNA Sequencing 03-25-2014, 09:32 AM
Replies: 6
Views: 1,754
Posted By shirley0818
How to merge/compare RNAseq data using different protocal

Hello,

I have RNA-Sequencing data generated from Illumina HT2000 for 14 samples from the same tissue. The technician applied the same protocol for these samples except for the last sequencing step...
Forum: RNA Sequencing 03-25-2014, 09:15 AM
Replies: 5
Views: 1,788
Posted By shirley0818
Got it. Thank you!

Got it. Thank you!
Forum: RNA Sequencing 03-25-2014, 06:39 AM
Replies: 5
Views: 1,788
Posted By shirley0818
Thanks both of you for your quick reply. ...

Thanks both of you for your quick reply.
GenoMax, the protocol used in our project is 7 samples mixture each lane from lane 1-7 in each flowcell. For each sample, there will be data generated from...
Forum: RNA Sequencing 03-25-2014, 05:44 AM
Replies: 5
Views: 1,788
Posted By shirley0818
How to keep the raw .fastq.gz files for RNASeq data

Hello,

I have 75bp paired-end RNASeq data generated from Illumina HTSeq 2000 using the protocol of 7 samples mixture each lane from lane 1-7 in each flowcell. Each sample has 6bp-index associated...
Forum: RNA Sequencing 02-03-2014, 05:48 AM
Replies: 1
Views: 1,048
Posted By shirley0818
TopHat generates accepted_hits.bam files for some of my samples, but for other

Dear Group,

I have run TopHat 2.0.9 and 2.0.10 for my 75 PE RNA-sequencing data. Totally, I have 8 samples sequenced on each lane on Illumina HiSeq 2000.

My problem is I got accepted_hits.bam...
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