User: SP

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SP250
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250
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Germany
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5 months, 3 weeks ago
Joined:
4 years, 10 months ago
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Posts by SP

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Genome structural annotation (augustus)
... Hi @kay, thanks for the input. I am looking for Maker independent solution. ...
written 5 months ago by SP250
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Genome structural annotation (augustus)
... Hello all, I am doing structural gene annotation and using augustus as a tool. While it works quite nicely on most of the cases it shows some miss annotations. One example i shown in the image, as RNA-seq shows that there are no introns present but augustus annotate introns. I have created intron, ...
augsutus gene annotation genome assembly written 5 months ago by SP250 • updated 5 months ago by Kay0
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Comment: C: How can i get only the upregulated and downregulated genes from chip-seq peak fi
... This paper explains and compares multiple the differential chip methods [Paper][1] [1]: http://bib.oxfordjournals.org/content/early/2016/01/12/bib.bbv110.full ...
written 2.9 years ago by SP250
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Comment: C: Tools to identify enhancers from chromatin marks
... I am not sure how much peaks shape and hight will help, every histone modification has it's own pattern. Of-course there are difference in shape or intensity of peaks on enhancer and promoter but for me combination of histone marks is a better proof. I would like to know what fellow-researchers thin ...
written 3.0 years ago by SP250
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Answer: A: Tools to identify enhancers from chromatin marks
... I have not used any tools but an easy thing could be to do a overlap between e.g. H3K27ac and H3K4me1 and found the overlapping regions, these are the most likely enhancer marks. You can do a heatmap for H3K27ac peaks and compare the occurrence of H3K4me1 and H3K4me3 around these peaks. you can use ...
written 3.0 years ago by SP250
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Comment: C: How to break broad peaks from H3K9me2 ChIP-Seq?
... 45kb and 32kb wide peaks, those are very big regions. I don't know what is your factor of chipping (transcription factor or histone). Of course, if you have such big region then you will have multiple genes associated with it. Easy fix could be to find TSS of a gene which is closest to the peak summ ...
written 3.0 years ago by SP250
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Comment: C: How to break broad peaks from H3K9me2 ChIP-Seq?
... One peak belong to multiple gene, you have to be clear (may be paste small part of list here). while annotating a peak, most of the people consider the nearest TSS for gene annotation. you have to ask her, is there a reason for annotation with two genes? She might have given two genes for intragenic ...
written 3.0 years ago by SP250
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Answer: A: How to break broad peaks from H3K9me2 ChIP-Seq?
... I agree with sinji, you call peaks with MACS2 and without --broad parameter it will give you narrow peaks. Regarding calling for differential peaks, there are multitude of options. [This paper sums it up quite well.][1] Just to give you an idea, it is really important to have replicates of chip-seq ...
written 3.0 years ago by SP250
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Comment: C: How can i get only the upregulated and downregulated genes from chip-seq peak fi
... I am late for the reply, as you already know now ChIP-seq does not give you up and down regulated genes, it only provides binding sites of your factor of interest (transcription factor or co-factor) basis on which you can look for gene's which are directly bound by your factor and potentially be dir ...
written 3.0 years ago by SP250
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Answer: A: representation of chip enrichment in two genomes
... You can plot a line plot with the tag densities of region. Centre of the plot could be the middle of the peak or TSS of gene. An example could be like in image, Red line represent enrichment on Human and purple could be for Mouse. ![enter image description here][1] [1]: https://s32.postimg.or ...
written 3.0 years ago by SP250

Latest awards to SP

Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to calculate P-value for biological repeats of ChIP-qPCR?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Analysis for Unknwon motifs obtained from Meme or Dream.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to predefine Chipseq peak calling peak length in MACS?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For heatmap.2 has become very slow in plotting heatmap.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For heatmap.2 has become very slow in plotting heatmap.
Student 2.9 years ago, asked a question with at least 3 up-votes. For heatmap.2 has become very slow in plotting heatmap.
Scholar 3.1 years ago, created an answer that has been accepted. For A: How to get nucleotide sequences for a given list of genomic positions.
Appreciated 3.1 years ago, created a post with more than 5 votes. For TPM for ChIP-seq normalization
Student 3.1 years ago, asked a question with at least 3 up-votes. For TPM for ChIP-seq normalization

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