User: Sachin Pundhir

Reputation:
60
Status:
Trusted
Location:
Denmark
Twitter:
@pundhir_sachin
Scholar ID:
Google Scholar Page
Last seen:
5 months, 1 week ago
Joined:
2 years, 1 month ago
Email:
p**********@gmail.com

Posts by Sachin Pundhir

<prev • 5 results • page 1 of 1 • next >
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Tutorial: Accurate prediction of active enhancers using PARE
... We recently developed a computational method ([PARE][1]) to **P**redict **A**ctive **R**egulatory **E**lements - enhancers and promoters. Here, I present a step-by-step tutorial of PARE usage, and its strength in accurately predicting active enhancers. More specifically, I evaluate PARE performance ...
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Comment: C: How to identify a certain pattern for histone marks
... Hi Carlos, Thanks for reporting the bug. It seems like using syntax "&>>" to redirect output is not supported in some shell versions. I have now made a new version of PARE (v0.05), replacing "&>>" with "2>&1" (more accurate way to redirect). PARE v0.05 is available for do ...
written 22 months ago by Sachin Pundhir60
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Comment: C: How to identify a certain pattern for histone marks
... EDIT 1: Yes, link is correct. EDIT 2: Yes, it requires two replicates. However, you can pass around it by passing the same bam file as two replicates. As you can imagine, this would although compromise on the robustness of results. EDIT 3: Yes, definitely, we have used it on H3K27ac also. If you h ...
written 22 months ago by Sachin Pundhir60
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Answer: A: How to identify a certain pattern for histone marks
... We have made a method for this purpose PARE ( http://spundhir.github.io/PARE/ ). In our experience, it should work well for your purpose. UPDATE: PARE is now published. It can be accessed here: http://nar.oxfordjournals.org/content/early/2016/04/19/nar.gkw250.abstract ...
written 22 months ago by Sachin Pundhir60
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Comment: C: How to analyze exome Copy number variation in single patients and in populations
... I think $name at step 3.2 need to be replaced with actual file name. ...
written 2.1 years ago by Sachin Pundhir60

Latest awards to Sachin Pundhir

Appreciated 20 months ago, created a post with more than 5 votes. For A: How to identify a certain pattern for histone marks
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: How to identify a certain pattern for histone marks
Scholar 22 months ago, created an answer that has been accepted. For A: How to identify a certain pattern for histone marks
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to identify a certain pattern for histone marks

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