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Hi, I am using Cutadapt 4.9 version installed in an conda environment. I have some follow questions and I am getting confused on how to trim the adapters. I have adapter information from the paired en…
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My problem is that I am having difficulty obtaining a list of variants using bcftools mpileup and bcftools call with PacBio data. I do not have this problem with data of Illumina paired-end sequencing…
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Hi,
We have a pipeline utilizing ABRA and want to update it to incorporate ABRA2. We have a list of indel realignment targets and use that along with an array of k-mers for realignment in our curre…
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Not much Nanopore data has been run using the pipeline, so it's hard to say how appropriate the default parameters are for these data vs Illumina. However, some suggestions based on the [`setDadaOpt`]…
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Hello,
I've been using [bionode-ncbi](https://github.com/bionode/bionode-ncbi/blob/master/lib/bionode-ncbi.js) to get SRR ids from a `PRJ**` IDs so I don't have to look for each file individually (ex…
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### Description of the bug
I think the problem might be the format (using .list or .bed formats) that I used to use in intervals parameter and I do not know the correct format (even after reading the…
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Hi,
I'm relatively new to bioinformatics and microbiology, and I've been following the DADA2 tutorial to process my 16S gDNA & eDNA sequencing data. After merging my paired reads and constructing …
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**Bug Description**
I have recently installed an Illumina iSeq-100 benchtop sequencer in my lab, and it was announced allready in 2018, that there will be a 2x 250 bp sequencing cartrige available so…
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Hi,
I'm using bcftools to call and filter markers for a haploid biparental population of 118 individuals. I have Illumina sequencing for all progeny. After indexing my reference genome (one of the …
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Hi,
I am hoping to perform transcriptome assembly using both nanopore long read sequencing data and illumina short read sequencing data. It appears RATTLE only permits the use of long read sequenci…