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Forum: RNA Sequencing 06-28-2018, 09:04 AM
Replies: 1
Views: 1,243
Posted By seqprone
What can you learn about your samples just by looking at normalized read counts?

Hi everyone,

My study involves multiple cell lineages which were isolated from the mammary gland and sorted based on surface markers. The FACS data 100% agrees with published literature and what...
Forum: Bioinformatics 02-28-2018, 09:52 PM
Replies: 0
Views: 1,255
Posted By seqprone
GSEA Leading edge analysis fails with gene set not found error

hi all!

I'm trying to run a leading edge analysis on my RNASeq data.

Hi everyone!

I'm trying to run a leading edge analysis on my RNASeq data using GSEA

I first create a ranked gene set...
Forum: Bioinformatics 07-30-2017, 07:19 AM
Replies: 11
Views: 8,028
Posted By seqprone
Could you please explain how you 'redid the...

Could you please explain how you 'redid the reference'? Thanks!
Forum: Sample Prep / Library Generation 10-10-2016, 06:16 AM
Replies: 1
Views: 833
Posted By seqprone
Pooling 'very small' patient samples for ChIP Seq

Hi everyone!

I've gone through a lot of threads regarding pooling of samples for sequencing. Unfortunately, I'm not confident if they address my concern.

My experiment design requires...
Forum: Bioinformatics 11-14-2015, 01:08 PM
Replies: 12
Views: 38,732
Posted By seqprone
Is there a way I could extract a range, say...

Is there a way I could extract a range, say [chr3,a,b] to a BED format from a BAM file?
Forum: General 10-23-2015, 01:15 PM
Replies: 5
Views: 23,639
Posted By seqprone
Ok! I'll try A&C but as a concept, I'll keep what...

Ok! I'll try A&C but as a concept, I'll keep what you said in mind. It's one thing to score on a multiple choice quiz and another to know the 'right answer'. Thank you so much again for your help!
Forum: General 10-23-2015, 12:57 PM
Replies: 5
Views: 23,639
Posted By seqprone
Thank you for the answers! unfortunately, I...

Thank you for the answers!

unfortunately, I still didn't get the right answer.

Both A and C are wrong =(

for the question :

What does the “log2(fold change)” in the gene differential...
Forum: General 10-21-2015, 12:09 PM
Replies: 5
Views: 23,639
Posted By seqprone
What does the “log2(fold change)” in the gene differential expression testing result

What does the “log2(fold change)” in the gene differential expression testing result mean?

A) Its the log-ratio of FPKM values for a pair of expressed genes.
B) Its the log-ratio between mapped...
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