User: dimitrischat

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dimitrischat50
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Posts by dimitrischat

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Comment: C: Deseq2 Shrinkage or no?
... Thank you very much for the answer ( that didnt involve ironic comments ) ! ...
written 17 days ago by dimitrischat50
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Comment: C: Deseq2 Shrinkage or no?
... "People" gave an explanation regarding the q-pcr information i gave above. Whether it is scientific or not it doesnt matter. Thanks for the info though. ...
written 18 days ago by dimitrischat50
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Deseq2 Shrinkage or no?
... Hello all, I am trying to do an analysis for differential gene expression for rna-seq data, cell line hela for different time points. For example this is 6 to 0 hours. People told me to do the analysis with no shrinkage but i dont believe its the right way to do it for example a gene with shkrink ...
rna-seq written 18 days ago by dimitrischat50 • updated 18 days ago by Friederike2.3k
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Comment: C: Merging Peaks from macs2
... They kind of recommend that you dont? What do they reccomend? ...
written 5 weeks ago by dimitrischat50
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Comment: C: Merging Peaks from macs2
... Sorry..will do! chr1 713706 714672 967 10.18 13.67773 8.27315 11.37243 macs2hisat2_peak_1 nm0k27_rep12 chr1 824823 825324 502 3.73 4.20165 3.50376 2.17421 macs2hisat2_peak_2 nm0k27_rep13 i now used the bedtools sort as @Devon Ryan said and then used what @ATpoint said. Now i got a merg ...
written 5 weeks ago by dimitrischat50 • updated 5 weeks ago by finswimmer6.0k
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Comment: C: Merging Peaks from macs2
... there are broadPeak and gappedPeak along with the excel thingy.. :D which one should i use? ...
written 5 weeks ago by dimitrischat50
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Merging Peaks from macs2
... After macs2, you get files such as .xls. I have 6 .xls files (0h,3h,6h each of them have 2 replicates) and i want to merge them so i can use them (and the bam files) into CSAW for Differential Binding Analysis of ChIP-seq peaksets. So my workflow is like this: I open the xls file, delete first row ...
chip-seq written 5 weeks ago by dimitrischat50 • updated 5 weeks ago by RamRS18k
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Comment: C: Using Diffbind R-studio
... Thanks a lot for your reply/help. Merging the peaks, you mean all 6 (in my case) into 1? If CSAW is easier i will use that. Is there any help/examples for that? ...
written 5 weeks ago by dimitrischat50
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Using Diffbind R-studio
... Total noob here. Differential Binding Analysis of ChIP-seq peaksets is my main goal, so i found Diffbind. I have 3 samples(single-end), 2 replicates each ( 0h, 3h, 6h), so in total 6 fastq files. First I used bwa mem for mappin, then samtools view to convert sam to bam, samtools sort, samtools markd ...
chip-seq written 5 weeks ago by dimitrischat50 • updated 5 weeks ago by Devon Ryan85k
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Comment: C: gff file of constituent enhancer For Young algorithm
... H3K27Ac histone mod - Human (RPMI-8402) cells. Do i call them with macs2? I am sorry but obviously i am a newbie ...
written 3 months ago by dimitrischat50

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Popular Question 3 months ago, created a question with more than 1,000 views. For from txt to bed
Popular Question 3 months ago, created a question with more than 1,000 views. For Editing Bed file
Supporter 11 months ago, voted at least 25 times.

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