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First of all, thanks for posting all that work in github and congratulations for a very good and useful tool. A quick question following the issue with DADA2's orientation of sequences after merging F…
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As you were saying, @VSack, that the positions currently reported by MDAsim seem very inconsistent, we should opt for simply substituting the current `position = ` with something like `original_positi…
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Hi,
I used dada2 for longer read than usual 300bp. The overlap of forward and reverse primers produces 444bp reads. So, my ASV length is 444bp. Usually i got 4000 to 5000 ASVs for 300bp length. Ho…
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Hi,
I was hoping to use this tool to simulate some reads for a set of amplicons. However, it gives me an error when I try it:
```
src/simulator.py linear -r ~/R/projects/umi.sim/nanosim.input.fasta…
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As promised - here we go... ;)
Hi,
I found out that in my dataset (paired-end fastq from Illumina), around half of the sequences is reverse complemented in regards of the actual selection library …
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Hi there,
The preprint for Distanced - https://www.biorxiv.org/content/biorxiv/early/2018/09/24/423186.full.pdf - has just been released.
Big take-home message on their benchmarking is that DADA…
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I'm planning to use DADA2 to denoise sequencing data of a very short barcode sequence (20bp). Aside from changing the minLen parameter is there anything else I should do?
Thank you for your attenti…
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groot$ filebutler
fb: info -d my-old-ztmp -size +10G
total 545G in 41 files
Endophyte_AR3060_AR3018_RNA-seq 221G in 18 files
GBS_ASW 140G in 11 files
GBS_WhiteClover_G…
afmcc updated
6 years ago
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Hi,
I get follows error when running the CRISPResso with Mixed mode (Amplicons + Genome).
```
ERROR: ("free variable 'df_genes' referenced before assignment in enclosing scope", u'occurred at index…
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When a dada object contains only invalid denoised pair-combinations for any one sample `mergePairs` fails with (at least to me) hard to trace errors. Different errors depending on whehter `justConcat…