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Hi,
I use the following command to map transcripts to my individual nanopore genomic reads:
`./minimap2-2.17_x64-linux/minimap2 -c -x map-ont -G4000 -F4000 -g4000 -r4000 --hard-mask-level -M 0 --s…
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Dear VariantBam developers,
I ran the command `variant $bam -m 100 -o mini.bam -b` to obtain a maximum coverage of 50 along my sample, however when I visually inspected the result in the genome bro…
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**Is your feature request related to a problem? Please describe.**
When trying to analyze nanopore sequencing data with CRISPResso2, the runs fails due to insufficient memory. I believe this is arisi…
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Hello.
I am currently using cDNA sequencing data, and when I tried to upload reads on ucsc, I found my reads representing the strand information in opposite way (I am very postive that all of the s…
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Dear author,
Previously, I used hapdup to get the diplod assembly based on ```Assembly.fasta```. Dose shasta new version support diploid assembly?
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## Is your feature request related to a problem? Please describe
At the moment there is an input option to use only [short reads](https://nf-co.re/mag/usage#direct-fastq-input-short-reads-only).
…
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i am doing nanopolish-eventalign for my nanopore direct RNA sequence reads.
I have 9 samples, for a sample the command is running for more than 24 hours and is not able to complete within time limits…
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Hello!
I wonder if you could let me know what tags the remapped BAM should be equipped with.
I want to customize some parts of the source code so that svviz2 may remap reads with the mappers o…
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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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Dear Heng,
I am trying to assemble a mixture of PacBio and Nanopore reads using minimap2 and miniasm, what would be the best switch for the overlap step? I tried minimap2 -t 32 -X -Hk15 -w5 -Xp0 -m10…
jflot updated
6 years ago