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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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Hi RSEM Staff, I work with miRNA pipelines and would be interesting to run RSEM estimations, especially due to miRNAs small sequence and the high number of hits. I was trying to run the protocol using…
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Hi Reza,
I've noticed that in this version of miRador, RPM normalization is applied by default. While this normalization can be useful, it may inadvertently remove low-expressed fragments that hold…
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The major issue in my case is the sample datas…
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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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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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How can one generate a custom annotation a file like
> MIRZAG/data/hg19_tree.nh
When I use the AlignmentExtraction (https://git.scicore.unibas.ch/SmallRNAs/AlignmentExtraction) pipeline (…
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Hello,
I have uploaded multiple fastq files in order to do the mapping for smallRNA.
All jobs finished with errors
![Screenshot 2023-06-20 alle 17 33 31](https://github.com/bioinfoUGR/sRNAtoolbox…
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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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Dear developers:\
Thanks for developing the software!\
It's hard to obtain the `blastall` nowadays because it was discarded from ncbi-blast. So I installed the software using Anaconda.\
The commend…