Taylorain

In the SAM tags, are m5C and m6A RNA modifications represented as "m" and "a," respectively? Is this the same for BAM files?

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Hi! **In the SAM tags, are m5C and m6A RNA modifications represented as "m" and "a," respectively? Is this the same for BAM files?** While using Dorado for methylation detection...

Hello, I’m using StringTie to process my Direct RNA Sequencing (DRS) data, and I have a few questions regarding the usage of certain parameters. Below is the command I used:...

m6A and Inosine Overlap in Basecalling Results

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Dear Dorado Developers, I am using Dorado for basecalling and detecting RNA modifications in my DRS data. Here are the commands I used: ```bash dorado basecaller \ -x cuda:0 \...

Hello, Thank you for providing and maintaining this fantastic tool! I am using salmon quant to quantify reads mapped with minimap2, and I encountered an issue when filtering alignments by...

Feature request / question: Convert VBZ-compressed pod5 to ZSTD-compressed pod5 not supported in 0.3.34

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## Description I am trying to convert an existing `.pod5` file that uses VBZ compression to a `.pod5` file using ZSTD compression using the `pod5 convert` CLI. For example, I...

Error in psiPerEvent: "Unexpected number of fields. 6 expected, 5 given"

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Dear SUPPA developers, I’m encountering an error when trying to compute PSI values using the psiPerEvent subcommand. I suspect it’s related to the format of either my .ioe or expression...

Inconsistent number of reversed matches (`qry begin > qry end`) between two servers running the same analysis

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Hello, I encountered an inconsistency when running **** on two different servers, using the **same genome sequence** and the **same custom library** with otherwise identical parameters. --- ### Environment A...

Dear RepeatMasker Developers, I am currently working on a repeat annotation project and I have a few questions regarding redundancy, curation, and accuracy assessment, as discussed in Issue #290. **Recommended...