kallisto pseudobam producing bin files... not bam... how to fix?
I posted about this issue in the git for kallisto ( https://github.com/pachterlab/kallisto/issues/286 ) but I am trying to determine what to do in the meantime. Why would I be getting an output with a *.bin instead of a *.bam ?
Ultimately, I need the read counts re: what fragment is being ascribed to what via the kallisto algorithm as I have non-canonical mitochondrial ncRNA that have sequence similarity with another gene and must figure out a statistical method for properly ascribing reads to transcripts.
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Is that an unfortunate spelling error on programmer's part? Have you tried to rename
.binto.bamand checking withsamtoolsto see if it is indeed a BAM file?