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Hi,
I have multiple 30X WGS data and want to try AA on it. As mentioned in other issues, 30X is too large for AA and downsampling is recommended. But I'm not sure which one is the right way for downs…
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> python /home/arkg/EMIRGE/emirge.py emirge-output/ -1 ../../JdF_1362A_J2.573-2/reads/SSU_reads/JdF1362AcombinedSSU.fastq -f SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta -b…
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I tried to install shorah via bioconda (conda install -c biconda shorah) and executing shorah will give the following error:
`pkg_resources.DistributionNotFound: The 'shorah' distribution was not f…
heylf updated
4 years ago
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I keep seeing the presence of an unknown taxa with the name "V1" anytime I construct my taxa bar plots. However there is nothing in my taxanomy.tsv file that traces back to this "V1" taxa and it seems…
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As the deblur require uniform length and usually there is a parameters to trim sequences, I am wondering for the trimming process, whether deblur firstly did a alignment and then trim to the target le…
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Hello Benjamin,
I've merged sequence tables of several `dada()` runs (in summary around 680 samples) and I am running the `collapseNoMismatch()` right now and it takes quite a while (it's running f…
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Thanks a lot for the decontam package. i am extremely new to programming and i tried out decontam .
i started with the "iscontam" function
1) The first graph is a histogram which influenced my c…
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Hi,
The error "ZeroDivisionError: division by zero" is raised in Collapsinator.py, line 766, in collapsinator
counts['pc_uniq_dcr_kept'] = ( counts['number_output_unique_dcrs'] / counts['numb…
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Clair3 does not call 16 bp at each end of a reference sequence (https://github.com/HKU-BAL/Clair3/issues/257)
Supplement Clair3 calls with Bcftools mpileup/call?
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Hi Ben,
Apologies for the multiple questions. I ran singlem separately on my metagenome reads and my MAGs. I then separated each marker and clustered them using the default species-level identity. …