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Forum: RNA Sequencing 12-08-2014, 11:20 AM
Replies: 5
Views: 1,882
Posted By LP_SEP23
Coverage standards for RNA-sequencing

Hi,

As part of my new faculty appointment I am the faculty adviser for my department helping get off the ground an Illumina sequencing core for the university.

While trying to put together some...
Forum: Bioinformatics 11-16-2012, 11:45 AM
Replies: 1
Views: 1,932
Posted By LP_SEP23
lncRNA differential expression using RNA-seq

Hi All,
I have been doing RNAseq for differential expression using standard reference genome mapping and using EdgeR or DESeq to detect differential expression with no problem. I also have extensive...
Forum: Bioinformatics 10-09-2012, 07:07 AM
Replies: 0
Views: 869
Posted By LP_SEP23
How to display biological replicates in a single UCSC track

Hi All,

I have ChIP-seq experiment with 2 conditions and 9 biological replicates on each
I have no problem displaying the alignments for each replicate (usually as bigWig). Looking at replicates...
Forum: RNA Sequencing 09-14-2012, 10:24 AM
Replies: 1
Views: 1,662
Posted By LP_SEP23
Anyone wiht experience using MATS for alternative splicing?

Hi,
I am looking into analyzing differential alternative splicing after a treatment. I have 2 conditions (control and treatment) and 4 biological replicates on each. I have on average 75 million...
Forum: Bioinformatics 06-01-2012, 12:17 PM
Replies: 2
Views: 2,209
Posted By LP_SEP23
Extracting fastq from Illumina/Eland export?

Hi,
I was provided with some sequencing data that I want to run through my pipeline, and although my pipeline uses fastq, the data is in Illumina/Eland Export format.

Any tips on how to covert...
Forum: RNA Sequencing 04-30-2012, 12:08 PM
Replies: 36
Views: 26,408
Posted By LP_SEP23
What is good coverage on an RNA-seq experiment

Hi,

I just got my first RNA-seq dataset alignment results today, and I am wondering what would be considered a "good run".
This is a pilot experiment, whose objective is to determine how many...
Forum: Bioinformatics 03-05-2012, 11:21 AM
Replies: 1
Views: 2,415
Posted By LP_SEP23
What is a good mapping quality cutoff?

Hi
I am analyzing a ChIP-Seq dataset and was considering filtering reads based on mapping quality. I am not sure what threshold is the most appropriate in practical cases.

Also, I am really...
Forum: Bioinformatics 03-01-2012, 06:53 AM
Replies: 5
Views: 2,371
Posted By LP_SEP23
Anyone has experience with Bowtie2?

Hi All,
my name is Lucia, and I've been lurking around for a while but this is my first post.
I have a pretty big ChIP-seq experiment to analyze, and initially did the alignments with Bowtie. The...
Forum: Introductions 02-03-2012, 12:39 PM
Replies: 0
Views: 713
Posted By LP_SEP23
Hello!!

My name is Lucia
I am a posdoc at UPENN, dealing with NGS from Chip-Seq and RNA-Seq (soon)
data from mice after learning and other treatments that affect long-term memory.

I am new to NGS and...
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