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Hi @aametwally,
I'm currently working on a project investigating potential changes in gut microbiome over time (within a 24 hour period).
I feel this is likely more of an experimental design q…
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Hello,
This programme is very fantastic in my daily use. However, recently I found the fastq files trimmed after by cutprimers.py can not run correct by samtools mpileup programme. My analysis …
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Hi...
I am running SqueezeMeta and got an error at step 14
The whole error message was as follows
"Error running command: perl /home/anil/SqueezeMeta/bin/MaxBin/run_MaxBin.pl -thread 12 -contig …
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Hello,
I have just read the paper 'Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing' (Prodan et al., 2020) and the authors recommend not using maxEE filtering for 16s V…
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We are using this pipeline for both MSSPE as well as amplicon sequencing now, so should rename the repo.
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We have are performing amplicon Next Gen sequencing of Bisulfite converted DNA. We are interested in the methylation status at the CpG sites in our region of interest. For our analysis, we first perfo…
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Hi - after building pTrimmer, I can't seem to get it to work--it drops with a Segmentation Fault right away.
Here's my command, using fastq files generated by a MiSeq:
```
$ pTrimmer -l -t pair …
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Amplicon sequencing using a set of artificial, amplicon-specific primer. If a reads is beginning with this primer, it is a target reads, and artificial primer should be removed. Otherwise it should be…
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Dear Canu developers,
I would like to know if Canu may be suitable to assemblying tiling amplicon sequencing data, which are characterized by ups and downs in coverage depth, due to differential PCR …
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Dear all,
I am trying nf-core amplicon for 5 different multiple sequencing runs. It got the error at ancom-tax step.
```
Error executing process > 'ancom_tax (Nature-level2)'
Caused by:
…