User: firatuyulur

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firatuyulur170
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Posts by firatuyulur

<prev • 34 results • page 1 of 4 • next >
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Answer: A: Filter by Fold change in DESeq2
... There is a function, complete.cases(), in R that helps you to get rid of NAs. mydata[complete.cases(mydata),] will give you your dataframe with no NAs. Then you can apply any numeric filtering you like. ...
written 21 days ago by firatuyulur170
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Comment: C: Optimization of RNA-Seq data mapping with tophat2
... Last time i had scores like this, i tried trimming according to fastqc results and it improved the numbers a lot. ...
written 21 days ago by firatuyulur170
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Answer: A: From bam files to isoform read counts
... Try [sailfish][1] They are not the exact counts but would work for many purposes. [1]: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ ...
written 26 days ago by firatuyulur170
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Comment: C: macs2 normalization on broadPeak
... James thanks for the help. After this quick conversation I started looking at the regions of peaks on igv. I put the spmr called bedgraphs to igv and checked broadpeaks beds by eye. Still cannot strongly argue about it, I suppose you are right about peak calling normalizes while doing its job. ...
written 7 weeks ago by firatuyulur170
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Comment: C: macs2 normalization on broadPeak
... Isnt fold change related to the number of reads aligned to the peak? ...
written 7 weeks ago by firatuyulur170
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Comment: C: macs2 normalization on broadPeak
... So what you are saying is the signalValues that I see in broadPeaks file are independent of the read depth as those are the values obtained from a normalised peak calling and I can compare two samples according to their signalValues although they have different read depths? ...
written 7 weeks ago by firatuyulur170
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Comment: C: Zero expression in cuffdiff
... it is really hard to read this, could you edit this dataframe? ...
written 7 weeks ago by firatuyulur170
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macs2 normalization on broadPeak
... Hi, I have a number of atacseq bams and their total read numbers differ. I did peak calling with and without --SPMR for normalization and there is no difference between the two ......broad_peaks.broadPeak files. yet there is a difference in the resulting two ....broad_treat_pileup.bdg files. While ...
atacseq callpeak macs2 written 7 weeks ago by firatuyulur170 • updated 7 weeks ago by James Ashmore2.0k
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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 10 weeks ago by firatuyulur170
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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 11 weeks ago by firatuyulur170

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Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Is It Fastq Format

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