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Hi,
I am using rentrez to get metadata for a large batch of sequences in the nucleotide database. I would also like to easily download the publications attached to each sequence, found online as A…
arw36 updated
7 years ago
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Hi, I am trying to run Breseq/0.31.0 on some evolved bacterial isolate Illumina data (resulting from experimental evolution) which I am trying to compare to its ancestral strain via consensus mode, an…
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Hi everyone! As we get ready for the event this weekend, I'd like to start preparing potential issues that team members can take on. To help with that (and to start getting to know each other), could …
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Hi Chris,
I have generated the Cluster_scgs.freq file (file size 4109754) and when I tried the variant_filter.py script I got this error, do you have an idea of what is going on? N is null?
Thanks…
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I like the dada2 approach and I think it greatly enhances how we evaluate NGS data.
I understand how the dada2 algorithm makes unsupervised "OTUs"/sequence variants or whatever we call them. The pr…
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The "_snp.txt" files contains information about original scientific publication for SNPs. However it might not be straightforward to find the correct publication. More information about those papers n…
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NTR
1) phospholipase B secretion phenotype (is_a protein secretion phenotype)
2) altered phospholipase B secretion (is_a phospholipase B secretion phenotype)
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Hi,
I tried to run MGAP in the following way
```
MGAP.sh -r none -s ../estimate/out_NtC_001879_r1.fq ../estimate/out_NtC_001879_r2.fq -l no
Reference = none
Only strain ../estimate/out_NtC_001879_r…
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When OTUs don't map...in microbial studies many times due to strains... Can we create a direct patching system or 'ADD to OTT' so that we can directly map them? Another study where everything has bin…
hdliv updated
8 years ago
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Can you possibly add a template for a PairedEnd RNAseq experiment?
And a single end alignment using the genome file that has the ERCC spike ins appended?
Also would it be possible toupdate the cur…