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I'm working with samples and having issues at the merge step (I'm losing ~75% of my reads at that step). I want to look at some denoised read pairs to see if I can identify the problem. If I have the …
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Dear all,
We have been using Lotus2 to analyse Illumina 16S data and have a question regarding the AmpliconShortPE option in the sdm config file.
Until now we used AmpliconShortPE T, as recommend…
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**Describe the bug**
I am trying to align CRISPR-edited genomic amplicons to my amplicon reference template. When I align these amplicons to its reference using minimap2, I get 10,000+ reads aligning…
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Hi guys,
Thanks for developing this great suite of tools. I have a question regarding the applying UMI_tools extract to identify cell barcodes from what is essentially an amplicon sequencing ex…
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I am trying to map paired-end reads from an amplicon sequencing using Bismark. The command line is
bismark --un --ambiguous --maxins 1000 --non_directional --score_min L,-0.6,-1 bismark-genome…
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In the example you have the following:
```
gunzip -c reads.fastq.gz | chopper -q 10 -l 500 | gzip > filtered_reads.fastq.gz
```
Is this what you would recommend for the default settings? I'm…
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Hi,
I am having some troubles with some 16S V3-V4 region paired-end reads. It has been pooled in 4 libraries which I have received back demultiplexed into the pools containing my samples (about 30…
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Hey,
This seems like a very nice tool.
I wanted to use it for demultiplexing a paired-end MiSeq run (ITS2 amplicon sequencing) where we used custom 8-nt CDIs as i5 and i7 and an additional 4-nt ba…
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First of all, thank you for implementing such a great tool and responding to all these issues!
While running the pipeline on 48 soil samples of 16S V3-V4 amplicons, I became slightly worried about …
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(crispresso2_env) YudeMacBook-Pro:NGS shwan$ CRISPRessoPooled -r1 PE-reporter-seq-LGC16574_L2_1.fq.gz -r2 PE-reporter-seq-LGC16574_L2_2.fq.gz -f AMPLICONS_FILE_PE_reporter.txt --name ONLY_AMPLICONS_24…