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Crispresso 2.0.23
Total region analyzed 18227 using CRISPRessoWGS
Similar message for all genomic regions.
Running CRISPResso on region #1/18227: /home/pankum/miniconda3/lib/python2.7/site-packag…
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The spline curves don't give the detail needed to see the individual amplicons. Use a stepped line chart. For the overview, perhaps a stacked chart to show the channels.
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Hi All,
I would like to use 'nanopolish variants' to call SNPs in MinION data. We have sequenced one long amplicon target obtained through PCR amplification. If I understand correctly I should ski…
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Hi,
I recently came across oligotyping and decided to try it for a bacterial mock community I sequenced via Pacbio Sequel platform. I have to state that my amplicons are **NOT** 16S, but a non-codi…
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Environment: CentOS6.5, Python 2.7.11, CRISPResso installed from source (master.zip downloaded from github), needle, flash and trimmomatic are in the CRISPResso dependencies dir.
Data was downloaded…
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Hi,
While using swarm on dereplicated seqs using vsearch i got the following error
**Vsearch output**
Looks fine
```Dereplicating file ../files/merged_fasta/ALL_combined.fa.gz 100%
127085163 …
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Hi,
I am using Minimap2 for mapping full-length 16S rRNA amplicons obtained with nanopore to a reference database. The mapping quality obtained is 0 for the majority of the alignments, only a few o…
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Hi there, I have tried to upload my biom file with the metadata included (as you instructed) and it won't upload. The upload bar moves from the left to the right but nothing happens afterwards.
Biom …
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I am trying to evaluate the effect of dada2 on individual amplicons as they are processed into various steps in the pipeline. Specifically, if say I have a sample of 4000 forward and 4000 reverse read…
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Hey,
I'm trimming each of my samples separately because of the issue with the empty sequences.
By doing so, I could see the output of BBMerge, which turns out to perform badly compared to PEAR:
`…