I want to extract differential expressed genes using LIMMA from RNA seq data for three cancer types viz breast, lung and prostate. These data should have tumor and normal samples. I have read some papers which have used data from TCGA. BUt now TCGA has linked to Genomics Data Commons and all data are not open access. All BAM files are under controlled access. Also, LIMMA requires raw read counts for analysis. I an new to RNA seq data and analysis. Can anyone help, where should I get these data and what format should it be, as I have read that TPM, FPKM normalized values cannot be input to LIMMA.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
I'm not sure what you'll have to do to get your data, but I can give you some advice on the RNA-seq part.
If you're starting with BAM files that means your reads are already aligned, if you start with reads (.fastq) you can map them yourself using any splice aware mapping tool. Assuming you have bam files though, you'll want to use a tool that extracts raw counts from the bam files. You'll need an annotation file (.gtf or gff format probably) and a counting tool. htseq-counts or featureCounts (in the RSubread package) are both good and widely used tools for extracting raw counts from BAM files, so start there and extract your counts.
Once you have gotten that far, then there are alot of tools like limma, deseq2, or edgeR that can use that data for analysis.
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
22 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
50 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment