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Dear all,
I would like to know if there is a way to properly visualize methylation information obtained from modkit in IGV genome browser (testing IGV 2.17 snapshot).
In particular, I ran Dorado wit…
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**Version info**
- bcbio version (bcbio_nextgen.py --version): 1.2.2
- OS name and version: Ubuntu 18.04.4 LTS
**To Reproduce**
- Exact bcbio command you have used
/usr/local/bcbio/anaconda/…
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### Description of the bug
I am running the most current version of @marchoeppner dev branch on Tower on a real dataset. The workflow passed repeat masking and produced the `consensi.fa` file but fai…
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Hi
i tested BitMapperBS recently ,it was really an ultrafast and memory-efficient aligner.
i runned the software successfully.but i have same problems with the output. the output didn't contain Met…
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Hello,
I ran the code `python /dir/bs_seeker2-build.py -f MyGenome -d /out/dir/ --aligner=bowtie2 -p /u/local/apps/bowtie2/2.2.9`
In MyGenome there is a contig named Seg3751.2; however, the index…
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Hi!. I ran bwa-mem2 to map a paired-end mode reads using the package of nf-core sarek by a nextflow process. I dont know exactly why but the process has no errors. However, the output sam file is empt…
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Would it be possible to handle ambiguous reference bases properly? That would increase the alignment quality for viral use cases.
Thank you.
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Hi, it is my first time to use Modkit to extract modified base signals but have some problems.
I use Dorado v0.7.1 to do SUP + modification calling (m6A,pseU).
I use minimap2 to align the unaligne…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.9
- OS name and version (`lsb_release -ds`): Red Hat Enterprise Linux release 8.5 (Ootpa)
**To Reproduce**
Exact bcbio comman…