Is It safe to convert .bam to .fastq and re-do the analysis?

Question

[jomagrax]

Hi everyone!

I've been given .bam files and asked to re-do a RNA-seq analysis, I have converted the .bam files to .fastq files with samtools, but I'm am afraid this could carry errors in downstream processes. Is this an actual problem?

Thankyou in advance, Jose

Answer 1

[GenoMax]

As long as your BAM file contained unaligned reads (and they were not hard-clipped) you should be able to use the dataset you made above since it should be equivalent to the original files.. You may need to take of duplicates, if you had secondary alignments.

[jomagrax]

I found the original sequences in the SRA repository, but thanks anyway!!