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Hi,
I have two libraries that I am having problems with the bacteria_tradis mapping for. I have used cutadapt to trim the transposon (and adapters) from the reads and selected only the reads that c…
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```
In version before 0.3.2, PerM didn't allow mapping reads shorter than 25bp with
seed F2. PerM didn't allow mapping reads shorter than 20bp with seed F1. In
both situations, PerM can be much slow…
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Input data file a: Aligned reads file obtained from mapping short reads to a reference genome
Short reads means that only gDNA reads, Right?
Thank you very much.
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Hello Alex!
I have a question about short read mapping. I have 76bp paired-end fastq. When I using total DNA fasta as reference sequnce, uniquely mapped read % was more than 80%. In this time, howe…
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Hello,
I'm trying to run OPERA-MS using this command:
`perl /home/arvodnev/OPERA-MS/OPERA-MS.pl --contig-file /home/arvodnev/test_project/AssembledSR/SPAdes/contigs.fasta --short-read1 /home/arvodne…
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Hi Alex and all!
I am going to handle some short sequence reads, which may be ~20bp or even shorter.
Is it still appropriate for mapping such short reads using STAR by tuning some parameters?
T…
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### Problem Description
We are currently decontaminating the short reads using `bbduk.sh`. Would it make sense to decontaminate the long reads as well?
### Problem Solution
I've seen certain …
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Hello! Thanks for your helpful tool!
I am trying to assemble long-read sequencing data with short-read polishing. My long read data (nanopore direct RNA sequencing) are from the animals under 25 de…
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Hi, I'm trying to genotype an SV VCF with Delly and getting this error:
```
Error: Delly genotyping requires local SV assembly (INFO/CONSENSUS) and breakpoint (INFO/CONSBP) introduced in delly v1.1.…