which bam file select to invert fastq file?

christopher-vollmers / Mandalorion

Pipeline to identify isoforms from full-length cDNA sequencing data

MIT License

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which bam file select to invert fastq file? #4

Open JXAUDZF opened 6 months ago

JXAUDZF commented 6 months ago

I have two type of bam files:1. D192-longissimus.flnc.bam(Split and remove the CCS sequence with primers, further filter to remove the multi transcriptional chimeric sequence)；2. D192-longissimus.fl.primer_5p--primer_3p.bam(CCS sequences that have been split and primers removed).Therefore I don't know which bam file should select to invert to fastq file as an input file.

christopher-vollmers commented 6 months ago

You want to convert the split file with primers removed. Ideally, you also want to trim the polyA tail from those reads if they still have it. Mandalorion has a tool for that. It's described in the README.

JXAUDZF commented 6 months ago

Thanks,FLNC BAM is ideal bam to fastq