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Hi there,
I have generated BAM files for all my samples manually using minimap2, what would be the format to pass these onto`sc_long_multisample_pipeline`? I see options listed for passing the FAS…
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Hello!
during the alignment process with `minimap2` I suffer from a very large memory consumption for only one of the 20 threads I use. I investigated what could be different in this thread and the o…
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Hi,
I am trying to use ampBinner_10X.py on my fastq and getting errors on the alignment step. Could you please comment on that?
Thanks!
Running code:
```
ampBinner_10X.py --in_fq P.fastq.gz -…
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Hi Wenjie,
I have meet some problem when using `wgatools paf2maf`. It could worked with minimap2 and anchorwave PAF output, but it failed with FastGA and wfmash alignment now. I checked the alignme…
baozg updated
2 months ago
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Hi,
I ran the ```dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v2``` modified model from Dorado. And I use modkit to generate the bed file including 4mC and 5mC positions using this command:
```
mod…
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Hi,
Thanks for this super nice method and the pipeline. In the minimap2 bam outputs, I don't see any junction reads even though minimap2 is run with the `-x splice` parameter. Sashimi plots are all…
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Hello!
question in the tittle, since minimap is "deprecated".
Thank you
ghost updated
2 years ago
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Hello,
I'm having an issue with running the lifton software. I'm running it on an HPC environment using 100GB memory and a computer node that has 2000 cores. The below bash script has the command I…
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Hi All - having many jobs fail with this type of error, which seems to indicated perhaps something about a poorly formatted fasta file? One issue is that I can't seem to find the offending file `GCF_0…
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Hello,
I am trying to compare the performance of different mappers on long reads and minigraph has unexpectedly low accuracy. I'm mapping 1 million simulated HiFi and R10 reads to the [HPRC](https:…