User: rleach

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rleach120
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Posts by rleach

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Analyzing digital gene expression data (DGE) from drop-seq pipeline with Seurat.
... So my question is "what are 'appropriate columns and rows'"? Does it include requirements imposed on column and row names? I was following a vignette for seurat and it clearly made assumptions about the row names (expecting mitochondrial genes to have row names that start with "MT-"). Plus, there a ...
written 7 months ago by rleach120
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Comment: C: Established conversion tool for a split-seq-generated sparse matrix market forma
... Basically, I want to either write a shell script that is accompanied by a conda environment with the necessary tools that users can install in their accounts on our cluster and run or else provide a galaxy workflow that does the same thing. I could include an R script I suppose, but that just doesn ...
written 10 months ago by rleach120
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Comment: C: Established conversion tool for a split-seq-generated sparse matrix market forma
... Yes, I saw that it has a read10x method that seems like it would work. Unfortunately, the current galaxy wrapper doesn't have that incorporated. I just added a comment on a galaxy issue to add that as a supported input type. In the meantime, I'm still hoping to find either a command line utility ...
written 10 months ago by rleach120
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Established conversion tool for a split-seq-generated sparse matrix market format to tsv (for input to seurat)?
... I've seen R and python code for doing this conversion, but (for setting up a pipeline) is there an established command-line utility and galaxy tool for converting the split-seq output (sparse matrix market format) into a format that can be supplied to the seurat galaxy wrapper (which appears to take ...
rna-seq written 10 months ago by rleach120
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Comment: C: Help understanding why filtering for unmapped mate isn't working
... Thank you so much!!! ...
written 15 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 15 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 15 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 15 months ago by rleach120 • updated 15 months ago by colin.kern930
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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 19 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 19 months ago by rleach120

Latest awards to rleach

Appreciated 18 months ago, created a post with more than 5 votes. For A: Building Snpeff Database
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Building Snpeff Database

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