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Input requirements:
1. Count matrix of mRNA expression with samples in rows and genes in columns
2. Count matrix of smallRNA expression with samples in rows and genes in columns
3. Count matrix…
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I'm trying to run a smallRNA pipeline before running a degradome-seq pipeline. I've installed the ce10 genome and am running this on the MGHPCC cluster, which uses an x86_64 architecture.
When I ru…
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Hi Damien,
I really appreciate your small rna seq workflow. I am trying to test it for a paired small rna set to bulk rna set.
I am running into an error when I initialize the program as per yo…
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It looks like FASTP is not able to detect *automatically* the adapter at all for miRNA-seq data.
For example, FASTP is not able to detect *automatically* the adapter in the SE FASTQ file from https…
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Hello, I want to use this tool for miRNA analysis. It has been installed, but the following error was reported when running the demo data. What should I do to solve this problem?
`[2023-11-08T02:…
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Hi Alex,
Firstly thank you for the great development of this tool.
I have a question concerning the gene counts from the .tab output when I set --quantMode GeneCounts and more specifically how to …
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Recently, I used piPipes step by step using data in manual, I ran the small RNA-Seq part:
piPipes small -i Zamore.SRA.ago3_het.ox.ovary.trimmed.fastq.gz -g dm3 -o Zamore.SRA.ago3_het.ox.ovary.piPipes…
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Hi,
I ran mantee without specifying a transcriptome index, the program is supposed to create its own index but outputs the next message and dies instead:
"The provided transcriptome index does n…
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Dear COMPSRA team,
I am following your tutorial and the modules Quality Control and Alignment were successful both for an example datafile from yours and for an actual sample.
Now I am having troubl…
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Hi Julian,
I run the software on my own data on linux. The results seems weird. For example, in enhancers' output file, the first 5 lines is:
"
codelen nnei nind nnon npat nsite pCL pFN pCL2 pFN2…