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Please consider supporting the pairwise mapping format of minimap2:
https://github.com/lh3/miniasm/blob/master/PAF.md#paf-a-pairwise-mapping-format
Note that minimap2 also supports outputting SAM.…
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Hi,
I'm curious if it's possible to run npScarf with ONT reads aligned to a reference genome (consisting of unique contigs). I've aligned the long reads with `minimap2` to generate an indexed and s…
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Hi,
I have been trying to manually select the cutoffs by running "hist_plot.py". As I understand, we are supposed to select cutoff values from the count-read_depth image and manually change the "cuto…
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### Description of the bug
For some reson, canu is not running on ONT data (`GenomeSize` specified, reads provided with `LongFastQ`, `R1`, `R2` and `Fast5` are set to `NA`).
### Command used an…
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Hello, I'm getting a segfault when building the latest version: 817ba03fc19e0fb2076381eb9536ff99240bd468
Using this graphmap command line:
graphmap align --threads 1 --ref Chlamy_and_lambda.fa --…
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Hello there!
I have a question about the -M 2 option for identifying sample types using the barcodes.
I see that option 2 finds matched barcodes on both ends of sequence, and identifies pairs th…
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Hi, Thanks for writing such a complete MAN page! I have a quick question, I have a total of 6 samples, and all of them are single cell Nanopore libraries. I'd like both the transcript and gene quantif…
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I found issue #521 but none of the tips there helped in my case.
I am trying to run bactopia on WSL + Ubuntu, fresh install. Installed MambaForge as per the installation instructions, then installed …
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Hey,
Thanks for making an excellent tool
I'm reading some nanopore bam files, which don't have read pairs, only single long reads.
I am looking for the best way to get the alignment length an…
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Hi again!
I was trying to use Methplotlib to see if I can plot my Megalodon data for 6mA and 5mC. Simply converting my sorted BAM output using samtools to CRAM format and using that as an input is …