User: dorota.komar

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dorota.komar10
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Location:
Spain
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1 year, 1 month ago
Joined:
3 years, 1 month ago
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Posts by dorota.komar

<prev • 11 results • page 1 of 2 • next >
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Comment: C: DeepTools plot correlation image error
... Thank you a lot for your answer. I tried to use BEDfile under choose computtaion mode and I selected all the files used for correlation as all of them were bed files. I was comparing 5 different files and I got 5 different multiBigWig summaries. Some of them did not work (I assume there was upper/lo ...
written 14 months ago by dorota.komar10
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Comment: C: DeepTools plot correlation image error
... oh, and the history I sent from razu@o2.pl account ...
written 14 months ago by dorota.komar10
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Comment: A: DeepTools plot correlation image error
... Davon, thank you so so much! That is amazing. I have just shared the history with you. I was thinking that maybe this has happened because I don't have enough overlapp? I was also trying to perform plotHeatmapand even though the tools worked, the image I obtained doesn't really look ok. I have my Ch ...
written 14 months ago by dorota.komar10
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DeepTools plot correlation image error
... Hi guys, I am trying to make some nice images out of my ChIP-seq data. I want to compare regions bound by my TF with known histone marks occupancy sites. To that I wanted to use deeptools tool PlotCorrelation. I have a following error coming up. Any ideas about how to deal with it? Thank you a lt ...
chip-seq plotcorrelation deeptools written 14 months ago by dorota.komar10 • updated 14 months ago by Devon Ryan1.9k
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How to go back to sequences from MACS2 peaks
... Hi, I am playing with my ChIP-seq results. I would like to check if I have any overrepresented motifs in the places my transcriptor factor is binding. To do that I have to have sequences of the MACS2. Is there any easy way of doing that in galaxy? Like overlapping once again mapped sequenced from b ...
chip-seq macs2 bowtie motif analysis written 14 months ago by dorota.komar10 • updated 14 months ago by Devon Ryan1.9k
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Answer: A: MACS error while analyzing ChIP-seq peakes
... Thank you a lot! I will try with MACS2 callpeak :) ...
written 14 months ago by dorota.komar10
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MACS error while analyzing ChIP-seq peakes
... Hi, I am analyzing my ChIP-seq data. I am pretty sure I am following the workflow correctly, because I obtained nice results for one tissue type. In the second tissue type I, however, got an error while trying to use MACS tool. It is kind of surprising, because I can analyze the data fine while usi ...
chip-seq macs written 14 months ago by dorota.komar10
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Answer: A: MACS did not work - invalid literal for int() with base 10: '1:N:0:CAGATCTG'
... Thank you very much for your response. I tried the conversion of Inputs into BAM files, however the peak calling did not work: INFO @ Fri, 22 Apr 2016 08:33:00: # ARGUMENTS LIST: # name = MACS_Inflorescence_1 # format = SAM # ChIP-seq file = /galaxy-repl/main/files/015/336/dataset_15336509.dat # ...
written 2.2 years ago by dorota.komar10
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MACS did not work - invalid literal for int() with base 10: '1:N:0:CAGATCTG'
... Hi I tried to call peaks of my ChIP-seq with MACS but an error appeared: INFO @ Thu, 21 Apr 2016 15:31:51: # ARGUMENTS LIST: # name = MACS_in_Galaxy # format = SAM # ChIP-seq file = /galaxy-repl/main/files/015/336/dataset_15336509.dat # control file = /galaxy-repl/main/files/015/336/dataset_15336 ...
chip-seq macs sam invalid literal error written 2.2 years ago by dorota.komar10 • updated 22 months ago by Jennifer Hillman Jackson25k
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Answer: A: Bug in Cuffdiff in server Main??
... Have the same error! Is there any possibility to be noticed when it will be fixed? ...
written 3.1 years ago by dorota.komar10

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