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Dear Katherine,
We recently used Betascan2 on the datasets generated by Singhal et al. 2015 (https://science.sciencemag.org/content/350/6263/928.abstract). This dataset is composed of 19 Zebra finc…
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I would like to use `mmseqs taxonomy` to detect contaminations within a transcriptome assembly.
The transcriptome is from a metazoan organism. Contaminations are mainly bacterial. I would like to u…
ms-gx updated
3 years ago
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HMMER v3.1 introduced specialised command line tools ``nhmmer``/``nhmmscan`` like ``hmmer``/``hmmscan`` but focused on DNA. Quoting the manual http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf
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Hi!
I have fasta sequences from open regions (same cell lines) from mouse and human. I wonder what would be the best way to do differential motif enrichment analysis of this data with your tool, so…
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**Describe the bug**
When running gimme motifs with the following parameters:
gimme motifs -s 0 -f 0.5 -g mm10 --denovo Alluvial_open_GM.5.0.Forkhead.0008.bed Alluvial_open_GM.5.0.Forkhead.0008_gimm…
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While running tfi.scan I am running into the following error which seems to be related to (https://kb.iu.edu/d/aqsj). Any ideas what could be causing this? I am using human, hg38, reference genome and…
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-Just trying to use the standard Fragpipe tutorial steps to generate a spectral library from DDA files. I get most of it done I believe but the log has an odd trace at the end I'd like to know if it's…
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Hello,
I want to detect the network and target genes relying on the RNA-seq data. I think your tool (netZooR) may be helpful. I have installed it and Cytoscape on my linux platform successfull…
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IGV-ScanFold on Windows 10 Home (Version 10.0.19042) does not complete scans.
igv.log info:
```
ERROR [2021-03-07T15:29:32,523] [RuntimeUtils.java:88] Traceback (most recent call last):
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Hello,
I run funannotate compare and came up with no results in the GO enrichment tab.
I found this message in the log file; " GO terms not found in go.obo " and the go-enrichment file is empty bu…