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Hi,
I understand from your documentation that both R1 and R2 reads needs to be in same read length. However, my dataset (16S amplicon sequencing with 515FY-926Rjed primer) has below sequence length…
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If we define whole/complete/full sequences as those spanning the first base of the (germline) V gene until the last base of the (germline) J gene [as per https://github.com/airr-community/airr-standar…
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I've noticed that the SILVA classifier is built on each run of the pipeline, which seems like a waste of resources to me. Wouldn't it be better to add the artifacts to the Docker image? I realize this…
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I am having an issue with running some 16S amplicon sequences through DADA2. I have successfully run two other datasets before, but for some reason I have been having issues with the one I am currentl…
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A few data sets (ITS in particular) have enough variation in amplicon length that the resulting sequences are likely a mixture of:
1. Reads that can be merged (ends overlap with confidence)
2. And…
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Hi Mike! Thank you for posting that amazing tutorial on Amplicon Analysis. It has been so helpful for getting started in microbiome research. I had a question regarding loss of reads during the dada2 …
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Hi @lh3
I have noticed some weird insert sizes generated by bwa mem (default settings) followed by samtools sort and stats, when I map my 2x150bp Illumina metagenome reads against the megahit assemb…
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Dear Felix,
I have come across an issue when aligning amplicon based BS-seq libraries. The majority of the reads are aligning to only one strand: the complementary to the top strand:
Final Align…
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Hello –
I have a question about combining different sequencing runs, specifically illumina and 454 runs.
For reference - Samples Include:
• Hydrothermal vent marine samples, time series over 10…
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hi,Blatte.
I have a ampliseq data from illumina platform and try to call ITD by getitd, running the code:$python3 $getitd -reference $itdref -anno $itdanno GSH \
$I/Nova373-RDMT09-A144V1-PM2-2019…
moshl updated
4 years ago