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I have the sequencing data in Nanopore of a small amplicon (230 bp) of the HLA-C gene. One of the challenges I face is the low quality of the sequences obtained, as well as the fragmentation of the se…
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Hi @FelixKrueger
I had a question - more of a thought process - regarding deduping the fastq sequences before it reaches the aligner.
http://felixkrueger.github.io/Bismark/bismark/library_type…
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What reference should one use if there are multiple serotypes of a Virus. I understand that sequences belonging to each serotypes must be aligned separately but what if there is no RefSeq available fo…
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Hi,
I am running nanovar v1.3.2 (installed via bioconda) using nanopore reads from cattle genome.
I encountered the error when nanovar ran hs-blastn:
```
[05/03/2020 12:54:46] - INFO - Cluster…
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### Description of the bug
I added some options with the " --extra_star_align_args" command, however the pipeline stopped with the following command error:
```
EXITING: FATAL INPUT ERROR: dupli…
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I have short read data that is about 150bps. There is an insertion of 77bps. I can't get BWA or Minimap2 to create the insertion properly to human genome with the default settings. Is there a certain …
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Hello,
I am attempting to use PECAT for error correction of a Nanopore dataset. I have installed the latest PECAT version with conda. Here is my environment. I have chosen not to install Medaka or …
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Bonjour @drosofff
Merci pour la mise à jour du tutoriel STARTbio du cours analyse des génomes 2023. Je viens de le tester et il marche très bien. Pour info, le déploiement de la VM a pris 24' et l…
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### Description of the bug
If I add the strandedness in the samplesheet as 'auto' the pipeline skips several steps including alignment.
Running the same exact command, with the only difference b…
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Dorado produces basecalls in unmapped bam file. How can I check the modifications from this bam file?