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Hello,
I'm working with consensus sequences of amplicon sequencing. Some sequences are being subtyped as Unkown by sierra local, however there seems to be no problem with subtyping the same sequenc…
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Hi,
It's a powerful tools for data analysis.
I have a question when trimming primers from paired-end reads of amplicon. The sequencing data (e.g. forward_reads) likes: AAATTTaaaaaaaaCCCGGG and GGGC…
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Hi Josie,
I'm wondering if it will be better to change the remapping to the suggested approach used by salmon (i.e. map with minimap2 and salmon quant with -ont flag).
See a few discussions and tu…
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See: https://bugs.sgn.cornell.edu/trac/cxgn/wiki/ResetPrimaryKeys
and
https://wiki.postgresql.org/wiki/Fixing_Sequences
```
SELECT
'SELECT SETVAL(' ||
quote_literal(quote_ident(s…
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Hi,
we would like to know if we can set a threshold for number of reads we get per amplicon - to make a call around being confident or not about the results. Please see the figure A below: where we…
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I am trying out your ITS-workflow tutorial in a stepwise manner using my own dataset by adapting it for 16S V4 reads . However I encounter fastq reads with primer sequences still present after invoki…
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### What happened?
Hi! Recently, IDT has released the **V2** for Midnight primers. May I know it is possible to include the updated primer scheme in `wf-artic`?
IDT Midnight primer website:
https…
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Hello,
I am running into an issue where I cannot set the mapping quality filter to be less than 5. This is necessary for us as we have amplicon sequencing reads that have large structural variants an…
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Hey, everyone.
I am using DADA2 to analyse tick microbiome and I've come across a few roadblocks.
After trying everything to use both forward and reverse reads, trying to merge them and being un…
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Hi Xiyu,
I am trying to use DAUMI running on an amplicon sequencing data set with 1M reads for deduplication.
The first step of the run_AmpliCI cluster has been running for almost ten hours, bu…