User: yff

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yff0
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Posts by yff

<prev • 7 results • page 1 of 1 • next >
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batch effect in RNAseq analysis using tophat cufflinks pipeline
... Hi everyone, I am using tophat and cufflinks pipeline to do RNA seq analysis on my data. I am new to RNA seq. I guess there might be some batch effect in my RNa seq data. I am not sure how can I detect and correct for batch effect? Do you have any idea about this? Thanks, ...
tophat cufflink rna-seq batch effect written 10 weeks ago by yff0 • updated 10 weeks ago by kristoffer.vittingseerup1.6k
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Comment: C: which file and column outputted from Cuffdiff corresponds to each sample FPKM st
... Hi, I am using tophat+cufflinks(cuffquant+cuffdiff). I have the differentially expressed genes. I am lookin for the FPKM sd. Does any of cuffdiff output file contain this information? ...
written 10 weeks ago by yff0
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which file and column outputted from Cuffdiff corresponds to each sample FPKM standard deviation?
... Hello everyone. I am using cuffdiff command from cufflinks pipeline to find the genes that are differentially expressed between case and control samples. I have got several files outputted from cuffdiff. I would like to have the standard deviation of FPKM values of samples. I am not sure which fil ...
cuffdiff fpkm cufflinks sd rna-seq written 10 weeks ago by yff0
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problem wit unzipping fastq.gz file
... Hello everyone, I have a fastq file in .gz format. I am trying to unzip it but it fails and give the error of "unexpected end of file" . This fastq file has been obtained from illumina sequencer. I was wandering if something was wrong with the sequencer or the way that they have zipped the file. D ...
illumina fastq rna-seq fastq.gz written 3 months ago by yff0 • updated 3 months ago by JY Nam20
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Comment: C: tophat running does not complete properly.
... The genome is my index which is called **ToxoDB35**. I mean that is the name for out out of bowtie index. The exact command that I am running is as follows: tophat -p 8 -G ToxoDB35.gtf -o sample_thout ToxoDB35 SAMPLE_R1.fq SAMPLE_R2.fq ...
written 3 months ago by yff0
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Comment: C: tophat running does not complete properly.
... Thanks for your reply. Actually I have to use tophat because it is part of my research pipeline. Do you have any idea what is the issue? ...
written 3 months ago by yff0
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tophat running does not complete properly.
... Hello everyone, I am trying to use tophat to align my fastq reads to the reference genome. I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and read files are in the same directory. Here you can see the screen shot of my d ...
tophat alignment rna-seq bowtie written 3 months ago by yff0

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