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Hello,
I did resquiggling and got errors, so was trying to annotate raw files with fastqs.
And I'm keep having weird results from annotating.
I tried two times but tombo can read all the fast5 i…
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Hi,
For our application, we wish to map NGS RNAseq (Illumina PE) to long error prone Nanopore genomic reads. Could you please suggest some settings that we could adapt to make STAR capture these mapp…
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I have run the Falco using the following commands
falco --nano reads.fastq.gz
I am using nanopore reads. Html report says it is using the sanger/illumina encoding even though I have specified the na…
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Hello @lkuchenb ,
I wanted to ask if this tool can handle fastq reads from Nanopore or PacBio. With a different aligner I can run xHLA and HLA-LA. My question is mostly about Optitype. Will it be a…
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**the exact command you tried to run**
Feel free to leave any original paths, we don't have access to your system
srun -N 1 -n 1 bash -c "flair collapse -g /home/mbauer/genome/gencode.43.GRCh38.prim…
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Hi,
I read your interesting paper and wanted to try this pipeline. I have some circular DNA reads produced by the Circle-seq method and sequenced by nanopore. I am wondering if this pipeline would …
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Dear all,
First of all, thanks for this very nice development.
I just wanted to report the fact that on some quite heavy ONT runs from bovine, NGMLR followed by sort was very slow (about 4 days …
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Hi, I am working with Nanopore direct-RNA sequencing and found your tools really useful. However, while I was trying to use your BamSlam script to generate some summaries and figures for the alignment…
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Hi @cheny19,
I noticed the discription of NanoSim was a Nanopore sequence read simulator. And I wonder
harness a software to generate some Nanopore reads with given a genome or a fasta file . When I…