User: firatuyulur

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firatuyulur100
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Posts by firatuyulur

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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 9 days ago by firatuyulur100
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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 16 days ago by firatuyulur100
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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 22 days ago by firatuyulur100
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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 weeks ago by firatuyulur100
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multiple SRR in a particular FTP conflict
... Hi all, It might be a silly question but I need to understand this. I am working on some ChIP-Seq data and while I was downloading the SRA from geo, when I [clicked on ftp at very bottom][1] there are [multiple SRR coded folders][2], each holding an SRA file inside. The question is, there is only on ...
chip-seq written 4 weeks ago by firatuyulur100 • updated 4 weeks ago by EagleEye3.4k
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rMATS readlength difference
... Hi all, I am trying to work with rMATS to analyse splicing events. With the new version of rMATS, they started using STAR and it does not allow using fastq's with different read length. My fastq read lengths vary between 41 to 50. [Here is the link][1] for one of my fastqc results, which actually re ...
rmats splicing rna-seq written 6 weeks ago by firatuyulur100
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Comment: C: RNA-Seq analysis with standard p-value
... I think why you are confused is because you do not see the (-) sign at your padjval column. That (-) sign you are not seeing is there to show you 10's power. so when its -5, it is 10^-5, which is a small number between 1 and 0. when padj is 0, it is the highest significance value that you can get, s ...
written 8 weeks ago by firatuyulur100
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Comment: C: Cuffdiff output filtering based on significance
... If you have the gene names, forget about the XLOC column and go with gene names. ...
written 10 weeks ago by firatuyulur100
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Answer: A: Cuffdiff output filtering based on significance
... expression bar plot is a nice one. lets say your main data from cuffdiff is "cuff_data" and your filtered table is "my_significants_filtered". A warning: if you have a couple of hundred significantly differentially expressed genes, your graph will be too crowded. With using a better threshold for p- ...
written 10 weeks ago by firatuyulur100
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Comment: C: Methylation levels at specific sites
... it is annoying that the bed files used as example has 4 or 5 extra columns than what [my bed][1] file has. therefore, the suggested package could not help me. [1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsm605318 ...
written 10 weeks ago by firatuyulur100

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Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Is It Fastq Format

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