RSEM and Tximport
2
0
Entering edit mode
pthom010 • 0
@pthom010-23694
Last seen 19 months ago
United States

I have 30 FASTQ files that I used to create a de novo transcriptome in Trinity. I then aligned the reads back to the assembly using RSEM. This is an organism that does not have an annotated genome. Is it possible to use DESeq and upload my data via tximport? I have a text file with the URL to each recults folder but I am not sure how to import them.

RSEM tximport deseq2 • 812 views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 2 hours ago
United States

Yes, you can use RSEM => tximport (see tximport vignette for an example), and then tximport => DESeq2 (both vignettes have relevant code).

ADD COMMENT
0
Entering edit mode

Figured it out. Thank you.

ADD REPLY
0
Entering edit mode
@james-w-macdonald-5106
Last seen 17 hours ago
United States

The short answer is yes. One would assume that you read all the documentation that comes with Trinity, including say this page? Which tells you things about the output that might be important for you when you are thinking about using tximport.

If you haven't closely read the Trinity documentation, then you should probably do so. Trying to do something complicated without having exposed yourself to the complexities of what you are trying to do is suboptimal.

ADD COMMENT

Login before adding your answer.

Traffic: 816 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6