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For those of you who are new to this space, perhaps start here:
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads
For those who are expe…
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Hi @Huanle
I got this error when I run this command on test data:
python ~/Software/EpiNano/scripts/main/fast5ToEventTbl.py ~/Downloads/multifast5_1.fast5
Traceback (most recent call last):
Fil…
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Hi, I am not sure which value I need to give here to configure pipeline..Please suggest...
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A conda environment named MetONTIIME_env is created, where seqtk, porechop, pycoQC, Nano…
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Dear Micheal,
porechop step gets killed after 2 hrs start of analysis. I have tried to do Analysis for 28 Gb fastq.gz of M.Tb reads data on PC with 16 Gb RAM, 1Tb storage. I have tried to reinstall…
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In the QIIME workflow, I am trying to replace the very slow and not appropriate vsearch classification of long-read metagenomics sequencing (ONT) by minimap2 which is very fast for this kind of reads.…
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Hi,
I am new with Pomoxis and I am trying to run a polishing step on budgerigar transcriptomic data after genome reference-based assembly but I am getting an error in the step of generating consens…
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Hi Jon,
Thanks for the excellent pipeline. I finished my genome annotation with it. It works pretty well when I applied to RNA-seq analysis. However, when I did the single cell RNA seq (based on 10…
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The usage message for the primary sequence_handling script does not list the handlers by the correct number for each option. For example, NP_Quality_Assessment is listed as "17" but it is option 15 …
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Dear,
Does sunbeam support data generated from 16S rDNA amplicon sequencing or single molecule sequencing techniques such as Nanopore and BioPacific ?
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I am running the pipeline with only two samples (one per condition) but when I get to the R script-part of the Snakefile I get the following error (probably since R is missing additional inputs from t…