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Answer: Case and control in microarray/RNA-seq analysis
Comment: Publish a Letter in higher impact vs Research article in lower impact
Answer: BWA alignment
A: RNA-seq: How to know which paired reads come from the same original fragment?
What are chromatin states ?
Comment: Tissue-specific DEG analysis with DEseq2
Answer: BWA alignment
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Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
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aw7
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I do not think `samtools fixmate` and `markdup` are going to work on PacBio long reads. `fixmate` is for setting and repairing mate inform…
Comment: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
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Azra
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I see, thank you!
Comment: Publish a Letter in higher impact vs Research article in lower impact
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shenwei356
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From the perspective of a Chinese, I'd like to choose a letter in a famous journal with a high IF. If I'm a PI, I think they are both OK, I…
Comment: Publish a Letter in higher impact vs Research article in lower impact
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ATpoint
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This is off-topic here. I suggest https://academia.stackexchange.com/ Anyway, since hiring procedures in academia are much focused on IF a…
Answer: BWA alignment
by
Vahid
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Thank you very much for your assistance. The problem has been solved; it was an index issue.
Answer: Manual Assembly and Protein Translation, HELP, assignment revision
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Philipp Bayer
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You asked the same question before, and I told you about the reverse complementing (https://www.biostars.org/p/9594474/#9594475 ), and now …
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Zeng Jingyu
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Hi Nikki, I have to say that I didn't fully understand your question. You said "don't care the association between Instrumental Variable a…
Comment: RNAseq one control two conditions, shared and exclusive genes
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Mohamed Abderrahmane
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I'm not entirely certain about the difference, but I assume it yields similar results. The method you're currently employing seems faster a…
Answer: BWA alignment
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a.alnawfal.1992
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The error [main_samview] suggests that Samtools is expecting a SAM file header but isn't getting one. This often occurs when the pipe (|) b…
Comment: RNAseq one control two conditions, shared and exclusive genes
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matteo.levorato
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I mean, which is the difference between doing two separated analysis or doing a one single analysis since the results are slightly differen…
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
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t.fortunato.asquini
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Thanks for the quick response! Yes I know that including lib.size in the design is uncommon and I have doubts about this. However, after no…
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the python version is a more efficient and faster implementation, it says. I'm just not sure which assay and which layer to use?
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# GATK version: > The Genome Analysis Toolkit (GATK) v4.2.1.0 > HTSJDK Version: 2.24.1 > Picard Version: 2.25.4 # COMMAND FOR BQSR #…
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While running with this batch option batch --method wgs option. I have used this command " cnvkit.py batch tumor.bam -n normal.bam -m wgs -…
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chrchang523
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Why do you think ADMIXTURE supports polyploid input? (Note that this is an answer, not a comment.)
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