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Hi,
I am trying to work with Porechop to demultiplex my data. The libraries are a bit complex, and I would really appreciate some help here.
We are doing microbiome work, and our hoping to do 16s…
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Hi everyone
I have been working with the National Institute for Communicable Diseases (NICD) on some of their SARS-CoV-2 sequencing. I adapted the "variation" workflow to call variants in Illumina …
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Larger BAM/FASTQs=smaller intervals and vice versa, etc. Might want to adjust based on number of samples also.
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**Describe the bug**
I encounter tow type of errors while using CRISPResso2. The ERRORs are **quantification window ERROR** and **invalid characters ERROR**
I upload all the fastq.gz file [here]…
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Hi,
Thanks for a great tool. I am playing around with genotyping amplicon data from Nanopore sequencing. I can get Straglr to call certain STRs but not others, and I wonder if I need to do somethin…
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Hi I have a large amount of RNA-Seq samples available and was wondering if I can use xHLA for typing? I was not able to find mentions of RNA-Seq data usage in the paper or on the github page.
Coul…
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Hi,
I am just testing the tool on my FASTQ files and always getting an error "buffer overflow detected". What does it mean?
Do FASTQ files need any preprocessing (e.g. a header change)?
Sho…
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Hello,
I used a metagenomic approach to sequence SARS-CoV2 genome and the data were very good with 100% coverage and 422x depth converge.
now I want to assemble my reads and get the consensus sequ…
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- Two main data generation strategies: (1) amplicon sequencing and (2) shotgun sequencing
- At this time analysis one can choose calling variants or performing within-host evolution analyses inclu…
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I try to remove duplicates (up to 2 mismatches) from the example below running:
cd-hit-dup -i input.fa -o output.fa -e 2
cd-hit-dup retrieves 8 clusters, when it should be 2 clusters: A and B. Only p…