Question: Can't group samples in StringTie for differential expression
0
gravatar for CandiceChuDVM
3.3 years ago by
CandiceChuDVM1.9k
United States/College Station/Texas A&M University
CandiceChuDVM1.9k wrote:

Hi all,

I have performed StringTie for individual samples and --merge for all samples by implementing the following commands:

$ stringtie $PATH1/sample1.aligns.sorted.bam -G $ANNOT -p 20 -o $PATH2/sample1.gtf     
$ stringtie --merge -G $ANNOT stringtie_gtf_list -o $PATH2/merged.gtf

Now I am going to run StringTie using the -B/-b and -e options for each sample in order to estimate transcript abundances and generate read coverage tables for Ballgown.

However, I am not sure how to group my samples. For example, I would like to group all 9 samples into 3 different groups:

group1: sample1, sample2, sample3
group2: sample4, sample5, sample6
group3: sample7, sample8, sample9

Do I have to execute stringtie three times (one group at a time)? For example:

$ stringtie $PATH1/sample1.aligns.sorted.bam,$PATH1/sample2.aligns.sorted.bam,$PATH1/sample3.aligns.sorted.bam \
 -G $PATH2/merged.gtf -B -e -o group1.stringtie.out.gtf

Or can I run them all together by separating them with different labels as in Cuffdiff?

Thanks!

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by CandiceChuDVM1.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1601 users visited in the last hour