User: Seigfried

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Seigfried20
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Posts by Seigfried

<prev • 18 results • page 1 of 2 • next >
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RTrackLayer import bed without name and strand orientation
... I have a bed file like this ChrIII_A_nidulans_FGSC_A4 0 10 0.83700 ChrIII_A_nidulans_FGSC_A4 10 43 1.11600 ChrIII_A_nidulans_FGSC_A4 43 59 1.39500 ChrIII_A_nidulans_FGSC_A4 59 65 1.67400 ChrIII_A_nidulans_FGSC_A4 65 74 1.95300 As you can see there are no Strand name columns or ...
rtracklayer bed R written 15 days ago by Seigfried20
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Comment: C: Heatmap.2 giving specific color to a value and start gradient after
... Yes this is it! Didnt think of that. Thank you! ...
written 7 weeks ago by Seigfried20
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Answer: A: Heatmap.2 giving specific color to a value and start gradient after
... Hi Samuel any( sapply(data, is.infinite) ) [1] FALSE any( sapply(data, is.na) ) [1] TRUE any( sapply(data, is.nan) ) [1] FALSE There is no infinite value or NAN in the matrix. I thought that the hclust cannot plot the distance between samples because of too many NAs ...
written 10 weeks ago by Seigfried20
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Heatmap.2 giving specific color to a value and start gradient after
... I am trying to plot a Heatmap. My data is as follows. GO s_3d s_6d s_17d peptide metabolic process 4.71E-29 2.84828E-20 2.70719E-24 organonitrogen compound biosynthetic process 3.38158E-22 3.26674E-15 6.3903E-22 positive regulation of gene expression 0.057421474 negative regul ...
R heatmap.2 heatmap written 10 weeks ago by Seigfried20 • updated 9 weeks ago by e.rempel430
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Answer: A: ChIP-Seq TSS Line Plot
... Hello @Guangchuang Yu Is there any way I can isolate reads per a specific bin? For example between '-500 to 0' or between '-1000 to -500' ? Also can I change the size of the bin? plotAvgProf(tagMatrixList, xlim=c(-3000, 3000)) Can I change this interval i.e. the size of the bin? Something like axi ...
written 10 months ago by Seigfried20
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Submiitting my own sequence to NCBI
... Hello I wish to submit my custom gene sequences of different cultivars of oryza sativa. I was using Bankit to submit my sequence taking the help of this tutorial here at [Bankit][1] Bankit accepts gene start and end locations and also the corresponding feature names of known features. I want to s ...
ncbi sequence bankit written 10 months ago by Seigfried20 • updated 10 months ago by natasha.sernova2.5k
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Answer: A: ChIP-Seq TSS Line Plot
... @Guangchuang Yu Thank you. I could solve my problem successfully using ChIPseeker ...
written 11 months ago by Seigfried20
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Answer: A: ChIP-Seq TSS Line Plot
... @datascientist28 That is exactly what I was looking for although I don't know the format of how your diffReps_output_gene1_X1.txt looks like so that I can similarly modify my own files. I did not find what I was looking for in SeqMonk. Anyone knows if Seqmonk can do this? ...
written 11 months ago by Seigfried20
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Answer: A: ChIP-Seq TSS Line Plot
... Thanks for the replies. I also found Seqmonk [Link][1] useful. [1]: http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/ ...
written 11 months ago by Seigfried20
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ChIP-Seq TSS Line Plot
... Hi I am trying to compare the effects of 2 transcription factors. I have the initial data files in .bed format on which I used MACS to get output .bed files again for peak calling. My genome does not have a specific GTF file and it is not fully annotated so I only have a GFF3 file. AnnotatePeaks.pl ...
chip-seq written 11 months ago by Seigfried20 • updated 10 months ago by Fidel1.8k

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For ChIP-Seq TSS Line Plot

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