User: ChIP

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ChIP490
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490
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Netherlands
Last seen:
10 months, 3 weeks ago
Joined:
6 years, 7 months ago
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Posts by ChIP

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Comment: C: Best input sample (CNV)
... They have it, the point is should I use individual inputs or should I merge them all and use it. ...
written 13 months ago by ChIP490
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Comment: C: Best input sample (CNV)
... Hi, Yes, I meant copy number alterations or structural variants, as in, for example, changes between a germline DNA sample and that of a tumour that has a high level of genomic instability. ...
written 13 months ago by ChIP490
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Best input sample (CNV)
... Dear All, I have 3 input samples, and I want to compare them and find out which is the best input to be used for peak calling. These samples have copy number variation. Any help is appreciated. ...
chip-seq written 13 months ago by ChIP490
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Downloading genomic interval for hg38
... Hi, I want to download genomic information for hg38, that have following information: region gene exon/tss/intron/intergenic/CpG/nonCpG The idea is to get this in a table format and then use intersectBed to to get overlap between the ChIP-seq data and this genomic information file. How can I get ...
chip-seq written 17 months ago by ChIP490 • updated 17 months ago by Alex Reynolds26k
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Comment: C: Binning the genomic regions and counting reads
... Hi, Thank you for your answer, I have an additional question. How can I plot these numbers as an heatmap or average coverage profile. Thank you ...
written 20 months ago by ChIP490
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Binning the genomic regions and counting reads
... Hi, I have list of genomic regions: chr14 83053041 83062424 chr4 9160067 9223997 chr2 144458153 144467912 chr10 86819472 86833402 chr12 39614733 39641285 chr4 68608137 68629925 chr17 36334147 36408831 chr12 19306607 19314016 chr4 97531083 97537086 chr2 88351 ...
bed tool bash written 20 months ago by ChIP490 • updated 20 months ago by James Ashmore2.5k
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Identifying DEG from time course data without condition
... Hi, I have a a time course data for 7 time points with 3 replicates each and I would like to point out the clusters of genes that are differentially expressed in at least one group Vs others. Similar problems with control and treatment problems can be solved with DESeq2 but I don't have 2 conditio ...
deseq edger rna-seq written 2.0 years ago by ChIP490 • updated 2.0 years ago by b.nota5.4k
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User guide of FunPat
... Hi, Could anyone of you share the user guide for FunPat. Unfortunately I couldn't find it on internet. Thank you ...
funpat written 2.1 years ago by ChIP490
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Comment: C: Ensembl ID conversion for a specific build
... Thank you so much. The information and the link was very helpful. ...
written 2.1 years ago by ChIP490
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Ensembl ID conversion for a specific build
... Hi, I have ensembl gene Ids from GRCh37.70 and I guess I need to use ensembl genes 70. But unfortunately, I can only find this [link][1]in archive that leads to ensembl genes 75. I think I need ensembl gene 70. Could anyone help me with this. Thank you [1]: http://feb2014.archive.ensembl.org ...
ensembl geneid-conversion written 2.1 years ago by ChIP490 • updated 2.1 years ago by Denise - Open Targets4.7k

Latest awards to ChIP

Popular Question 11 months ago, created a question with more than 1,000 views. For Heatmap of Differentially Expressed Genes
Epic Question 12 months ago, created a question with more than 10,000 views. For Hypergeometric Test On Gene Set
Centurion 13 months ago, created 100 posts.
Popular Question 16 months ago, created a question with more than 1,000 views. For SNP zygosity from RNA-Seq data (BAM file)
Popular Question 16 months ago, created a question with more than 1,000 views. For Copy Number Variation from paired end RNA-Seq data
Popular Question 16 months ago, created a question with more than 1,000 views. For Heatmap of Differentially Expressed Genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Heatmap In R With Large Datasets
Popular Question 20 months ago, created a question with more than 1,000 views. For Heatmap In R With Large Datasets
Good Question 20 months ago, asked a question that was upvoted at least 5 times. For Plotting Reads Around Tss
Great Question 20 months ago, created a question with more than 5,000 views. For Heatmap In R With Large Datasets
Popular Question 23 months ago, created a question with more than 1,000 views. For Hypergeometric Test On Gene Set
Popular Question 23 months ago, created a question with more than 1,000 views. For Heatmap In R With Large Datasets
Popular Question 23 months ago, created a question with more than 1,000 views. For Normalizing Bam Files
Popular Question 23 months ago, created a question with more than 1,000 views. For Heatmap of Differentially Expressed Genes
Great Question 23 months ago, created a question with more than 5,000 views. For Heatmap In R With Large Datasets
Popular Question 23 months ago, created a question with more than 1,000 views. For To get genes for each clusters from heatmap
Popular Question 23 months ago, created a question with more than 1,000 views. For Confused With Peaks And Motifs
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Annotating Peaks To Ensemble Build
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Annotating Peaks To Ensemble Build
Great Question 2.1 years ago, created a question with more than 5,000 views. For Heatmap In R With Large Datasets
Great Question 2.9 years ago, created a question with more than 5,000 views. For Plotting Reads Around Tss
Great Question 2.9 years ago, created a question with more than 5,000 views. For Heatmap In R With Large Datasets
Appreciated 2.9 years ago, created a post with more than 5 votes. For Hypergeometric Test On Gene Set
Appreciated 2.9 years ago, created a post with more than 5 votes. For Plotting Reads Around Tss

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