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Hi,
I am trying to run Piggy for a couple of closely related bacterial genomes but the analysis fails during creation of the cluster files with “Cannot open output file: piggy/cluster_intergenic_fil…
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Hello,
I am trying to annotate a file of protein calls (i.e., a Prodigal metagenome output file) using microbeannotator. My file is 750M with 2,000,000 reads and an average sequence length of 275 …
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I want to download the database. I used the command that "enrichm data" .but the database not download automatically.
(enrichm) user@user-X11DPi-N-T:~/Desktop$ enrichm data
usage: enrichm data [-h…
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@jebrosen So I rerun the conda `RepeatModeler` with `-debug` with the following command:
>/usr/bin/time -v RepeatModeler -engine ncbi -pa $threads -database $genome -LTRStruct -ninja_dir /home/oushuj…
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Hello,
Curious to use this resource to try and genotype nuclei in a set of pooled samples of tissues from C57BL/6J mice. Number of samples in each pool ranges from 2-4. Nuclei are reasonably wel…
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Hi there,
I have completed an initial analysis using DiscoverY in the female+male mode, and I am wondering how I might determine whether the kmer size I used is optimal for the data I have. For the…
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**A reproducible template workflow for single-cell DNA methylation data**
DNA methylation is a heritable epigenetic mark that shows a strong correlation with transcriptional activity, and may be de…
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Hi @fenderglass and @aysegokce , this is Khi Pin. I've been trying to implement v0.1.2 in my WDL workflow (set to go public sometimes this month), but I've been running into errors where v0.1.1 had no…
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- [ ] concatenate and dereplicate phaeo proteins (or contigs?)
- [x] Use Salmon to map Tara meta T
- [ ] look at SNPs for pop gen?
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Hi,
I was trying to use IsoPhase do call SNPs from the Pacbio Isoseq data for a single sample. However, when I run the `select_loci_to_phase.py `with all the files required, I was keeping getting 0…