User: firatuyulur

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firatuyulur140
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Posts by firatuyulur

<prev • 26 results • page 1 of 3 • next >
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rnaseq data vs. phenotype
... Hi, I am given a set of RNASeq fastqs to carry out diff. expression analysis. I have 3 replicates for both control and treatments. I use bcbio for the pipeline that takes care of many steps. Aligner is tophat2. I used DESeq2 for the diff exp part. The results are not very satisfying that in wet lab ...
tophat2 deseq2 rna-seq written 16 days ago by firatuyulur140
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Comment: C: LASTZ does not accept/like "-" (dash) in Fasta file
... -i in sed will make a change in the original file, I'd rather go without -i for this case because we dont know what is needed to be done specifically. why is this post in job section anyways? ...
written 25 days ago by firatuyulur140
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Answer: A: Threshold of removing genes with low counts ?
... I do not think there is a certain threshold. When it comes to drawing a plot out of counts, the zero lines do make your computer suffer as there will be a couple of thousand 0 lines that I remove them directly. While analyzing, you will use differential expression, and there will be a p-value / p.ad ...
written 10 weeks ago by firatuyulur140
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Comment: C: How to plot a heat map for the top 30 differentially expressed genes.
... many plots automatically order the data alphabetically although you order them in a specific way. to save yourself from this you can first order your data the way you want. then try `my_data$ens_id <- factor(my_data$ens_id, levels = my_data$ens_id)` and then plot. ...
written 10 weeks ago by firatuyulur140
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Comment: C: Widening the distances between PCA vectors in PCA a biplot
... you could remove the black dot labels with `fviz_pca_biplot(res.pca, label ="var")` or you can simply get rid of black dots with `fviz_pca_biplot(res.pca, invisible ="ind")`. once you remove black dots, if you use xlim and ylim that only encircles your blue arrows. say your arrows are within the x a ...
written 10 weeks ago by firatuyulur140
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finding unique mutations from a multi-sample VCF
... Hi all, I have gone through many posts and couldnt find my answer. I have a vcf file of 4 samples. What I want to reach from it is the list of unique mutations among samples. Example, at position N their genotypes are as ; 0/1 0/0 0/0 0/0. In such case, this is a unique mutation for sample1 at p ...
vcf snp written 3 months ago by firatuyulur140 • updated 3 months ago by Pierre Lindenbaum96k
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Answer: A: I am a student, what can i do with 23andme raw data?
... You can check the meaning of each SNP, given with the rs code. There are plenty snp databases where you can detailly read about the effects of each snp. ...
written 4 months ago by firatuyulur140
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Answer: A: Plus and minus strands plotted together
... For the ones who have suffered from the same problem; Apparently, GRO-Seq figure is independent of the tool. It is possible to get a visualization as in the link above with any browser. I used [Homer][1] for GRO-Seq analysis. The trick is, when it comes to generating the bedgraph using makeUCSCfile ...
written 4 months ago by firatuyulur140
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Plus and minus strands plotted together
... Hi all, I am working on a GRO-Seq data and I want to plot a graph like [one these figures][1], plus and minus strands are reversely merged on the same line. I know that UCSC genome browser can handle this, but in many ways, it becomes user-UNfriendly. So does anyone know a tool or GUI which can plot ...
gro-seq figure chip-seq written 4 months ago by firatuyulur140
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Comment: C: multiple SRR in a particular FTP conflict
... yes, thats helpful but the thing is 8million spots for a chipseq data is kind of a low. Should I process them separately and then merge them? or merge the fastqs? I agree that there are 3 runs but not sure whether they are replicates, the three seem to be complementary ? ...
written 4 months ago by firatuyulur140

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Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Is It Fastq Format

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