SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
rethinking log-log RPKM plots BAMseek RNA Sequencing 6 12-22-2011 10:44 AM
Understanding Maq log output anna_vt Bioinformatics 1 10-17-2011 07:48 PM
Question to combine Bowtie output with Tophat's -- impact on Cufflinks FPKM values berath Bioinformatics 0 04-21-2011 08:38 AM
Question about Seqclean error log hammerf Bioinformatics 0 03-15-2011 09:43 AM
Maq output: assemble.log file contains what? soniat Bioinformatics 0 12-15-2008 06:25 AM

Reply
 
Thread Tools
Old 05-17-2012, 01:51 PM   #1
adumitri
Member
 
Location: Cambridge, MA

Join Date: Jan 2010
Posts: 27
Default Question about Cufflinks Log Output

Hi,

I was wondering if anyone could help me interpret the following part of Cufflinks' output:

Code:
> Map Properties:
>       Normalized Map Mass: 284238.81
>       Raw Map Mass: 284238.81
>       Fragment Length Distribution: Empirical (learned)
>                     Estimated Mean: 190.09
>                  Estimated Std Dev: 77.77
[12:23:09] Assembling transcripts and estimating abundances.
Do the Estimated Mean and Estimated Std Dev values refer to the insert size?
Our analyses involve paired-end, 100 ntd-long reads, and the values we calculated for (5 million reads of each of) our samples using bowtie2 and Picard tools are somewhat lower than the ones we get in the Cufflinks log. Consequently, I wanted to find out if the difference is something to worry about, or if it is just a consequence of not using the whole samples when estimating the insert size measures.

Thank you!
Alexandra
adumitri is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:26 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO