User: Researcher
Researcher • 50
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... 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 ...
written 11 days ago by
Researcher • 50
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... 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 ...
written 9 weeks ago by
Researcher • 50
• updated
9 weeks ago by
jared.andrews07 ♦ 5.5k
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... 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
Researcher • 50
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... 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 ...
written 11 weeks ago by
Researcher • 50
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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
Researcher • 50
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... Thanks @ATpoint for explaining it well. ...
written 3 months ago by
Researcher • 50
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... 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. ...
written 3 months ago by
Researcher • 50
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... 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
Researcher • 50
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... 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
Researcher • 50
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... 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
Researcher • 50
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