User: jesvinjoy35

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Posts by jesvinjoy35

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Comment: C: How to compare different chipseq peak calling methods?
... @jared.andrews07 by best I mean the most accurate ones. It doesn't matter for which factor. The tools I tested works well with both narrow and broad peaks. So, I would like to know if there is any way to calculate sensitivity, specificity and accuracy for each of these tools. I did try finding some ...
written 12 weeks ago by jesvinjoy350
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How to compare different chipseq peak calling methods?
... Hi, I have been using various peak calling methods like MACS2, JAMM, BinQuasi and Zerone across the same samples for transcription factors and for histone modification. JAMM works well with and without control samples and gives the highest number of significant peaks while all the other methods work ...
chip-seq written 12 weeks ago by jesvinjoy350 • updated 12 weeks ago by jared.andrews072.3k
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Comment: C: Is there any database to find housekeeping genes with two and three copy number
... @WouterDeCoster is there any database for this. I mean it should be having details of the gene, how many copies and its paralogs if any. ...
written 17 months ago by jesvinjoy350
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Comment: C: Is there any database to find housekeeping genes with two and three copy number
... Yes, it can have paralogs but the gene should be having two or three copies. Is there a way to find this? I know not all housekeeping genes could be having more than one copy but if I could get a list of two or three copy genes, that would also do the job. ...
written 17 months ago by jesvinjoy350
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Is there any database to find housekeeping genes with two and three copy number in mouse?
... I am trying to get a list of housekeeping genes with two and three copy numbers. Is there any database to find these genes. Please help. ...
gene copy_number written 17 months ago by jesvinjoy350
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Answer: A: How to prepare param.yaml file of GLEAN for gene predictions from Augustus and G
... After contacting the author of the tool, I came to know that this tool is no longer supported, The author himself told me not to use this tool. However, the answer to the question is given below. param.yaml: evidence: GeneModel: Augustus: types: "coding:AUGUSTUS" ...
written 17 months ago by jesvinjoy350
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How to prepare param.yaml file of GLEAN for gene predictions from Augustus and GlimmerHMM?
... Hi, I am trying to create a consensus get set using GLEAN. The input files I am using are gene predictions from Augustus, GlimmerHMM and GenScan. I have loaded the input files into MySql database. However, I want to know is there any syntax for the Augustus and GlimmerHmm gene predictions in the "p ...
assembly glean written 18 months ago by jesvinjoy350

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