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Answer: IGV track display problem: interval rectangle from BED file appears above all tr
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The problem was the filename suffix, it's meaningful in how IGV treats the file. It is .pk here, but changed to .bed and it works.
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> Any help is appreciated
You should consider upvoting and validating (accepting, green check mark) comments/answers you have received on …
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Thank you for your detailed reply
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- Merge bams - yes. (why do you have so many ?). Merging fastqs before creating bams is easier (cat *.fastq.gz ) than bam merging.
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There is a related discussion here: https://github.com/samtools/bcftools/issues/2142
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Without the presence of [**UMI**][1] in data, it would be difficult to say with certainty that a pair of sequences share an identical origi…
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I'll agree with GenoMax here. While the approach of bambu shares several methodological underpinnings with methods used for short-read qua…
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Data volume is going to depend on the amount of sequencing. Was this a PromethION flowcell? Tool should handle the data as long as you have…
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Did you see a recent thread --> https://www.biostars.org/p/9612865/ which delineates standard methods for short-read data.
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The overall size for all bam files is around 150 GB. Is this common for nanopore and does this tools handle this volume of data?
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How about using `modkit` provided by Nanopore for methylation data analysis: https://github.com/nanoporetech/modkit
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Will refer you back to my comment above. Don't be fixated on the Q scores. You don't say what kind of data this is but it may still align f…
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Because this question just received an upvote: I used `vt decompose -s` back in the days, but I think bcftools now also makes you choose th…
Comment: Significant reads loss after fastp
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SpliceAndScript
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I have attached the phred score image of my reads, your opinion will be appreciated.
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I have RNA-seq data and here I am attaching the fastqc report image of ![enter image description here][1]my reads before and after running …
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