User: Rose

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Rose0
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Posts by Rose

<prev • 15 results • page 1 of 2 • next >
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CUFFDIFF giving empty CDS.DIFF files
... Hi, I ran cuffdiff using c.elegans( WBcel235) gtf file on two groups of bam, ech having three replicates. The output produced by cuffdiff had empty cds.diff, cds.count_tracking and cds.fpkm_tracking. I have checked several sites regarding this issue and found that, the gtf file suppied should co ...
c.elegans cuffdiff rna-seq written 6 months ago by Rose0
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Comment: C: chip-seq "mock" and "control"
... Thanks for the fast reply Devon. ...
written 8 months ago by Rose0
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chip-seq "mock" and "control"
... I have been trying to do a chip-seq analysis. I have some questions. 1. What is "Mock" in chip-seq? This is what I understood. Mock is a sample which is immunoprecipitated, but is non-specific. Is that true? 2. If I have a 'Control' sample and an 'experiment' sample and a "mock" sample, Do I nee ...
chip-seq written 8 months ago by Rose0 • updated 8 months ago by Devon Ryan82k
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Comment: C: Biological significance of Fold_enrichment in macs2
... Thank you so much Devon ...
written 8 months ago by Rose0
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Comment: C: Biological significance of Fold_enrichment in macs2
... Thanks Devon! So, In case, if I need the negative enrichments, I should swap the control and chip sample files while doing peak calling? ...
written 8 months ago by Rose0
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Comment: C: Biological significance of Fold_enrichment in macs2
... Thanks Ian, I have one more doubt. I have run chip-seq experiments on mouse samples and did peak calling using macs2 by the following command. pol1_1.fastq is the control sample and pu1_1.fastq is the chip sample. `macs2 callpeak -t pu1_1.fastq_trim.gz_A1.bam -c pol1_1.fastq_trim.gz_M1.bam -n pu1_ ...
written 8 months ago by Rose0
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Biological significance of Fold_enrichment in macs2
... Can anyone explain me about the biological significance of fold_enrichment in macs2. ...
macs2 written 8 months ago by Rose0 • updated 8 months ago by Ian5.2k
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How is the fold_enrichment in macs2 calculated?
... Hi , This question has been explained in many posts, but am not able to understand it correctly. That's why I came up here. Can anyone please tell me how the fold_enrichment in macs2 calculated. Please explain with an example data set. Also, after the differential binding step using edgeR, again I ...
macs2 written 8 months ago by Rose0
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Comment: C: How to get Kegg pathway names from kegg pathway IDs
... So sorry for the late reply.. I was able to get the results by this way. Thanks a lot. ...
written 9 months ago by Rose0
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Comment: C: How to get Kegg pathway names from kegg pathway IDs
... This is the example data. GENE_NAME KEGG_ID 1. Klf6 NULL 2. Fer 04145, 04514, 04650, 04670, 04810, 05140, 05144, 05146, 05150, 05323, 05416 3.Itgb2l 04622 Expected Output : GENE_NAME KEGG_ID PathwayName 1. Klf6 NULL 2.Fer 04520 ...
written 9 months ago by Rose0

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