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STAR aligned BAM files

Hello all, I have 24 genome aligned BAM files using STAR. I donot have the fatsq files, and i want to have count of isoforms. I know i can use STAR with parameters to have that, but it seems that i cannot directly use these BAM files in STAR. Is there any way to do that?

genome_aligned star bam files transcripts
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updated by Ram Ram • written by rajdeepboral00 • rajdeepboral00

but it seems that i cannot directly use these BAM files in STAR.

You most definitely can.

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written by Ram Ram

2 answers

Use ' samtools fastq' to convert the bams back to fastq. See: https://www.htslib.org/doc/samtools-fasta.html

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updated by ATpoint ATpoint • written by Pierre Lindenbaum Pierre Lindenbaum

Side note: This assumes that fastq files were not trimmed or manipulated in the first place before STAR alignment and BAM files were not filtered or manipulated either. If not, then you can recreate the original files. Still, and I do not get tired saying that, a reproducible analysis requires raw data. Ask yourself why you don't have it and whether it, together with experimental methods and logs, you can get it to be publishable.

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written by ATpoint ATpoint

You cannot use STAR to get isoform level counts, only gene level counts and you can do that using an input BAM. For transcript level counts, use a quantification tool such as salmon/kallisto or RSEM

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written by Ram Ram

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