User: Ekalavya

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Ekalavya10
Reputation:
10
Status:
New User
Location:
USA
Last seen:
2 months, 3 weeks ago
Joined:
4 years, 3 months ago
Email:
m********@gmail.com

Posts by Ekalavya

<prev • 7 results • page 1 of 1 • next >
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Comment: C: deeptools plotProfile plots inconsistently
... Thank you very much colin.kern! It is the random starting points of the cluster. It will be good if can have control over this. I am using hierarchical clustering. I am also trying to find out the optimal number of clusters. ...
written 12 weeks ago by Ekalavya10
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Comment: C: deeptools plotProfile plots inconsistantly
... Sorry, somehow the image is not uploaded. it can be found here. https://i.ibb.co/c1ggNJc/profile-Plots.jpg ...
written 12 weeks ago by Ekalavya10
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deeptools plotProfile plots inconsistently
... Hi, I am trying to plot a few ChIP-Seq signals on a region set using deepTools plotProfile. I have been using this tool but it is only recently I observed this unusual behavior. When I plotted identical data 4 times the outputs are very different. When I checked the corresponding output bed files, i ...
plotprofile deeptools plotheatmap written 12 weeks ago by Ekalavya10 • updated 12 weeks ago by colin.kern900
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Comment: A: bedtools, merge function: avoid merging intervals if separated by a single base
... Thank you ATpoint. It worked for me! ...
written 3 months ago by Ekalavya10
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Comment: A: bedtools, merge function: avoid merging intervals if separated by a single base
... Hi gabri, did you find any workaround to this problem? I am in the same situation. I want to consolidate coordinates of all the Cs in my RRBS dataset. For this, I pooled (all replicates and groups) the CX-report from bismark and used bedtools merge to get unique locations. My final bed file contain ...
written 3 months ago by Ekalavya10 • updated 3 months ago by ATpoint34k
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length of Long interspersed nuclear element in the mouse genome
... rmsk primary table has > 5 million records for repetitive elements. There were 989434 entries belong to "LINE" class of repeat. When I checked the lengths of these LINEs, a majority of them (973906) were shorter than 5kb. I took the "genoStart" and "genoEnd" to calculate the lengths. Aren't these ...
genome long interspersed nuclear element written 14 months ago by Ekalavya10 • updated 12 months ago by Biostar ♦♦ 20
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Answer: A: Bowtie2 Output, Concordant Vs. Discordant Mapping??
... A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`). `--fr`/`--rf`/`--ff`: The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. ...
written 4.3 years ago by Ekalavya10

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