User: Researcher

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Researcher50
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Posts by Researcher

<prev • 74 results • page 1 of 8 • next >
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How to convert 10X single nuclear RNA Seq bam file to fastq?
... Hi All, I have 10X single-nuclear RNA Seq bam files and want to convert these to fastq files. I am not sure how can we do this? Will this be similarly treated as we handle scRNA Seq bam files using bamtofastq? Thanks ...
bamtofastq 10x genomics cellranger snrna written 11 days ago by Researcher50
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Looking for suggestions if ROSE can handle multiple samples together?
... Hi All, I am trying to use ROSE to call Super Enhancer between the two subtypes of a cancer, where each group has 5 samples. But I am not sure how to identify potential SE by handling multiple samples (together with ROSE) from each subtype and to compare these with the other subtype. Looking for any ...
rose super enhancer chip-seq h3k27ac written 9 weeks ago by Researcher50 • updated 9 weeks ago by jared.andrews075.5k
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Comment: C: Unable to convert single cell RNA Seq bam to fastq using cellranger's bamtofastq
... Thanks @genomax for your response. Yes I am using the same bamtofastq utility. Earlier with some previous set of data and the same command I was able to generate fatsq files in folders named with their unique ID but this time the same command has generated with “MissingLibrary” named folder. That’ ...
written 11 weeks ago by Researcher50
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Unable to convert single cell RNA Seq bam to fastq using cellranger's bamtofastq
... Hi i have a quick question, i have few aligned bam files from single cell RNA Seq data. I want to regenerate fastqs from them. In order to do so i am using cellranger's bamtofastq and I am also getting fastq files but in the specified path within a folder named “MissingLibrary_1_flowcellName”. I am ...
single cell cellranger single cell rna seq written 11 weeks ago by Researcher50
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Comment: C: GSVA for mouse scRNA-Seq
... Hey [oriolebatimore][1] I am also looking for a workflow to follow for my scRNA-Seq data, did you find any answer to this question. I will really appreciated if you can share some of your experiences related to this. Thanks [1]: https://www.biostars.org/u/18009/ ...
written 3 months ago by Researcher50
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Comment: C: Is there a way where we can convert TPM to raw read count?
... Thanks @ATpoint for explaining it well. ...
written 3 months ago by Researcher50
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Is there a way where we can convert TPM to raw read count?
... I have a GEO dataset which only has log2TPM values but for a downstream analysis I would require only its raw read count. Is it possible to back calculate the raw read count from TPM values? Kindly guide. ...
normalization tpm read count rna-seq written 3 months ago by Researcher50
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Comment: C: Seurat on both pooled and unpooled samples
... Hi [Kristin][1], I also have 5 samples from two conditions and struggling with the same concern you mentioned above. Did you get the answer to your question, will you mind sharing your experience with the problem? Thanks in advance! [1]: https://www.biostars.org/u/13153/ ...
written 6 months ago by Researcher50
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Comment: C: DiffBind to call differential binding of Super-enhancers from ROSE
... Hi [Jared][1] thank you for your reply. I just left a same question [here][2] , please have a look. I hope you meant the same? I am really stuck with this and looking for a way out. [1]: https://www.biostars.org/u/40195/ [2]: https://www.biostars.org/p/406421/ ...
written 7 months ago by Researcher50
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Comment: C: DiffBind to call differential binding of Super-enhancers from ROSE
... Hi [venu][1], I am a bit lost and seeking your help. Actually I have 10 bed files from 10 samples, each one has a different start and end coordinates based on their SEs. But I am confused about making a common bed file from all these together in order to generate the read count matrix. Before usin ...
written 7 months ago by Researcher50

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