User: eyonesi
eyonesi • 0
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Posts by eyonesi
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... hello
dear genomax
I used trinity/RSEM/edgeR pipeline for analysis. The quality check of samples and biological replicates step was done to ensure that my biological replicates are well correlated. The Pearson correlation and PCA method were used and heatmap and PCA plot were generated. Since the ou ...
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... hi
I run a project of denovo rnaseq with 3 treatment and 3 replicate for each treatment. I performed Quality Check Your Samples and Biological Replicates step for differential expression output by trinity/rsem/edger pipline, but replicates and treatment are not properly classified. how can i solve ...
written 1 day ago by
eyonesi • 0
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... Hi
I am trying to install trinity protocol but I don’t know how I can write following command with my directories.
export TRINITY_HOME=/path/to/trinity/installation/dir
I am new in Linux,
Please help me with the explanation of details of this command
thankyou
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Comment:
C: Bimodal GC content
... Hello, dear thackl
I was running a denovo rnaseq expriment on a plant.similarity, my fastq GC content result is bimodal. Is it possible for you to more explain about "the second peak corresponded to specific repeat class"? I think it is depended to existance of chloroplast genome, what is your idea? ...
written 10 months ago by
eyonesi • 0
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... thanks for your answer. Can I ignore all output even if it shows two peaks in gc content?
with regards
...
written 10 months ago by
eyonesi • 0
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... hello everyone
I am running denovo rnaseq experiment at quality control step. I can’t interpret and trim two plot duplication level and GC content at output of fastqc . I have read some articles that is not recommended to remove duplicates for differential expression analysis. I don’t know that ho ...
written 10 months ago by
eyonesi • 0
• updated
10 months ago by
Michael Dondrup ♦ 44k
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... Hi all Dear
what are minimum hardware requirements (RAM, Hard Disk, CPU, Graphic Card) for denovo RNAseq analysis, when it is avaiable 32 Gb raw data, Trinity pipeline? ...
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Comment:
C: to pool or not to pool
... dear WouterDeCoster
thank you
...
written 16 months ago by
eyonesi • 0
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Comment:
A: to pool or not to pool
... exactly I asked about pooling extracted RNA from replicates of each treatments to create libraries. So which one is better ' pooling RNA or not pooling? and also if we pool the RNA, isn't it complicate the analysis and assembly in a de novo analysis? ...
written 16 months ago by
eyonesi • 0
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Comment:
A: to pool or not to pool
... thank you st.ph.n
its OK I'm going to do DGE. but which method is preffered or is better? ...
written 16 months ago by
eyonesi • 0
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