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Following the DADA2 ITS tutorial (v 1.8), I was able to process our groups ITS amplicons (we amplified the ITS1-region using ITS1F and ITS2R primers; 2x250bp protocol). I found that we lose many (50-1…
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Hi,
I want to validate my bioinformatics protocol in analyzing 16S rRNA V3-V4 sequence. I was using the following mock sequences, [https://github.com/andreiprodan/mock-sequences] from [https://doi.or…
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@gkarthik after noticing drastic changes in the number of trimmed primer seqs between ivar 1.2.1 and 1.2.2, I came across your comment in https://github.com/andersen-lab/ivar/issues/42#issuecomment-62…
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such like DPA1 DPB1
DRA
DRB3
DRB4
DRB5
and DM or DO?
Even the quality is not that good for above gene, I really wanna see the possible call set.
Thanks
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Dear EBI developers,
First, thank you for the great work you're doing on this.
I am using the **development** branch and trying to run the wgs-single-reads pipeline. The sample input_example f…
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As I've found out, all R1 sequences must be of the same length. R2 too. Is it necessary to have sequences in R2 files synchonized with sequences in R1 file (same number and order)? If I trim all R1 fi…
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Hi,
I came across your package through an issue (batch effect) that I was trying to solve with Benjamin Callahan (dada2) - https://github.com/benjjneb/dada2/issues/876
Benjamin suggested that…
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There are empty sequence being added to trimmed fastqs. I ran the following command:
```
pTrimmer-1.3.2 \
--seqtype pair \
--ampfile amplicon_file.txt \
--read1 R1_paired.fastq.gz \
--trim1 R1_p…
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Hi,
I just finished running an existing pipeline, which I extended with pTrimmer to ensure removal of sequencing primers. The resulting data is now unfortunately improperly paired (i.e. the reads in …
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Hello,
I constructed simple mock communities comprised of short synthetic genes that vary only at a 6 bp region in the middle, combined in various known concentrations (example sequences of one suc…