User: rleach

gravatar for rleach
rleach120
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120
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Location:
United States
Last seen:
2 months ago
Joined:
4 years, 2 months ago
Email:
r*****@genomics.princeton.edu

Posts by rleach

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Help understanding why filtering for unmapped mate isn't working
... Thank you so much!!! ...
written 3 months ago by rleach120
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Help understanding why filtering for unmapped mate isn't working
... I'm sure this is a dumb question, but I've got a workflow in galaxy that trims adapters, removes duplicates, and then filters for quality and to get only reads whose partner is mapped. The following analysis complains that it can't find the mate for a ton of reads. I looked at the sam file and dis ...
alignment written 3 months ago by rleach120
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Comment: C: In Peak Calling, what is the input sample
... That's reassuring. Thanks. Is there a way to assess how good a control/input is? I basically want to figure out whether I should suggest that they change their procedure to sequence the input as their control. ...
written 4 months ago by rleach120
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In Peak Calling, what is the input sample
... Every time I've done a ChIP-Seq, or (as in this case) CLIP-Seq, analysis over the years, I have used the "input" samples and not used the "control" samples. Whenever I've had both, I would google the difference to see which I should use and everything always said to use the input in whichever case ...
clip-seq chip-seq written 4 months ago by rleach120 • updated 4 months ago by colin.kern750
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Comment: C: Any pitfalls to consider when using MACS on paired-end data when forward and rev
... Great. Thanks. Glad to hear it. ...
written 8 months ago by rleach120
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Any pitfalls to consider when using MACS on paired-end data when forward and reverse reads are different lengths?
... I have some paired-end data where the forward and reverse reads are different lengths (due to unrelated requirements of someone else's samples on a multiplexed sequencing run). Can I use the entirety of both reads when I predict peaks with MACS2 or should I trim the longer reverse reads? Are there ...
macs paired-end written 8 months ago by rleach120
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Tool: TreeView3 - An update to java TreeView
... Our first beta release is now [available for download][1]. TreeView3 is based on java TreeView. * Completely re-designed interface with one main data panel. * Now with clustering (no need for Cluster 3.0). * Flexible color and label settings. * Streamlined purpose (do one thing and do it well). * ...
app tool written 17 months ago by rleach120
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Comment: C: JAVA Treeview: analysing my favourite genes at once
... Find arrays refers to the columns. It's a search of the column labels. ...
written 19 months ago by rleach120
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Comment: C: JAVA Treeview: analysing my favourite genes at once
... If you can manipulate the tree to get the genes next to each other, you could select them and select Export->Save Data and then open that file for clustering? There's probably a better way to do it, but that's my first thought. ...
written 19 months ago by rleach120
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Comment: C: Java TreeView like tools
... It is being updated, in fact: http://treeview.princeton.edu. We're on the cusp of the first beta release. Final code review in process. Prepping publication too. ...
written 19 months ago by rleach120

Latest awards to rleach

Appreciated 7 months ago, created a post with more than 5 votes. For A: Building Snpeff Database
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Building Snpeff Database

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