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How to extract one modification at a time- used to use --call-code parameter?

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#589 3 comentarios 0 reacciones 0 asignados Ver en GitHub

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Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
35/100
Tipo de issue
Nueva funcionalidad
Claridad
Necesita aclaración
Estado de actividad
Estancado
Stack tecnológico
rust
Área
bioinformatics, cli

Línea de trabajo

Start with the modkit extract calls entry point and compare current command options with the historical --call-code behavior across releases. Check whether the current command offers a supported way to extract one modification at a time and review the memory and output-size concerns described in the issue. Done means the requested workflow is either supported and documented or the requirements for restoring it are clearly established.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

question

Hey!!

I have an aligned bam from direct RNA sequencing, and it has multiple mods attached to it (m6A, 5mC, 5hmC, and pseudouridine).

Around 6 months ago we ran into this issue where when we would use modkit extract calls to extract multiple modification from RNA data, it would create an insanely large bam and/or crash out on memory and couldn't finish the process because it was using so much RAM (even after throttling with setting threads, queue-size, and interval-size). I solved this problem by using the --call-code parameter and doing one mod at a time, decreasing memory and size of our output files.

Now, I'm noticing --call-code is not even a parameter or option anymore in the latest versions of modkit. I can't seem to figure out 1) what older version I was using 6ish months ago and 2) what versions actually had that parameter as an option.

If I want to use modkit and extract one modification at a time, is there another way to do so rather than just doing a awk command after it is complete? Or, can you tell me what was the last version to use --call-code so I can pull a respective container with the right version?

Lastly, is this something you can add back in? Because at least for us it was extremely useful and our bams were so large we couldn't even get the process to work without doing one modification at a time. Thanks!

Hailey Z

Lenguaje dominante
Rust
Estrellas
278
Forks
34
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