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Dear community,
According to the manual of MITObim, this useful software can use PacBio long reads for mitochondria assembly. Can I use Nanopore long reads, too? Thank you.
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First of all, congratulations on that fantastic tool for its speed.
I am not sure if "fastp" automatically detects adapters used by ONT libraries. And what would be the recommended flags to treat …
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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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conda is leveraged for installing (some) dependencies (at least, the recommended install method), but conda is not fully leveraged via a bioconda recipe for installing scNanoGPS.
Are there plans on…
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### Description of bug
(bio) zhisong@zhisongs-MacBook-Air spades % bin/spades.py -s ../accuvirnew/bad_nano/hiv_50_2k.fastq -o testfasta --isolate
== Error == /Users/zhisong/Desktop/accuvirnew/b…
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Dear RawAlign Team,
I am facing challenges in aligning raw signals generated using Kit14 chemistry. I ensured that the correct pore model was specified during the indexing process with the followin…
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Hi! I'm running long_read_typing.py for PacBio -reads for which I have extracted the HLA-regions (originally aligned data to chm13, then extracted hla with HLA*LA and ran bam2fastq). I was wondering a…
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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
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I have nanopore long-reads from tumor (tumor only)
I also have SNP/indel variant calls from the same sample from illumina in both germline (normal) and tumor data
I want to try and get phasing inf…
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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…