Dear Friend
Actually I have 2 questions
I got RNA-seq data of 3 sample. I did assembly by velvet_oases and Run TopHat mapping .Then (in order to compare result ) I also did assembly with Trinity . I perform read counting of each sample using (util/TrinityStats.pl) but I also need to perform read counting of each sample against the merged assembly. In trinity, is it (util/alignReads.pl) that perform read counting of each sample against the merged assembly? If it is not how can I count it in Trinity?
and my second question (that I have no idea about it )is how can I perform correlation analysis between biological replicates?
It is my first time I am using Trinity and I ' m bit confused. I very appreciate your suggestions and answer?
Regards
Mina
Hi Mina
Is expression level estimation what you want to do? Maybe for DE analysis?
If so maybe these page can guide you:
http://trinityrnaseq.sourceforge.net/analysis/abundance_estimation.html
http://trinityrnaseq.sourceforge.net/analysis/diff_expression_analysis.html
Best,
Juan
simple correlation analysis:
*get the vectors of count numbers into R
* put them together with cc
try bowtie align and the stats should tell how many reads are getting aligned ... if you need per transcript read count than cut -f3 bowtie.sam | sort | uniq -c will give you the stats. This can be then used in the R option as given by Michal
If you need the total number of mapped reads:
samtools view -c -F 0x004 mapped.bam
I think you need to first align the two assembly output to know what you can compare. Overall, I guess you want to use the best results of the assemblies. You will also be interested in annotate the assembled sequences. The last time I did this I used Trinotate for that.
Hope that helps a bit.
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