User: ashwinkelkar

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ashwinkelkar10
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Status:
New User
Location:
IISER Pune India
Last seen:
1 year, 11 months ago
Joined:
1 year, 12 months ago
Email:
a***********@protonmail.com

I work on X chromosome inactivation and the role of chromatin (long range) interactions in X chromosome function. I am interested in understanding how the chromatin conformation of the X chromosome facilitates silencing or escape from silencing.

I work on mouse embryonic stem cells and I use data from ChIP and RNA Seq studies to infer silencing efficiency on the X chromosome. I am making a foray into HiC analysis now.

Posts by ashwinkelkar

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Comment: C: Merging sam files for HiC analysis downstream
... Hello Sean Thanks for the prompt reply. I will go through these and try the one that is most appropriate. I chose HiCexplorer because the same lab that has put out this tool has also done the experiment for the dataset that I want to use. Thanks, Ashwin ...
written 24 months ago by ashwinkelkar10
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Answer: A: Error message produced by bowtie2 (HiC-Pro)
... This seems like an issue with your installation of bowtie though I am not exactly sure of this. You could get around this by using any other HiC tool that uses an aligner that is not based on bowtie2 or that can directly use output of bowtie2 run independenly. Try using HiCexplorer [(link)][1] This ...
written 24 months ago by ashwinkelkar10
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Merging sam files for HiC analysis downstream
... Hello everyone I am using a dataset for HiC analysis. The dataset is broken into 41 individual paired ended fastq files as the raw data. I want to merge the 41 (x2) individual sam files after alignment but I want to do so *without* sorting the reads and maintaining the header intact. Since this is H ...
hic align sam written 24 months ago by ashwinkelkar10

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