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christopher-vollmers / Mandalorion

Pipeline to identify isoforms from full-length cDNA sequencing data
MIT License
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whether can put .bam file as a input #3

Closed JXAUDZF closed 6 months ago

JXAUDZF commented 6 months ago

can fastq/fasta as a reads input, as well .bam file can?

christopher-vollmers commented 6 months ago

you can't use bam as input. If you have a bam, convert to fast using "samtools fastq". We need to align the reads using specific options and keep track what fasta/q file each read came from.

-Chris