Human brain samples (BAM files) differential gene expression

Question

[nermze86]

I have been handed 8 sets of RNA-seq data. These were already aligned, and are in BAM format. The alignment was done by an outside company long time ago, and i have no idea what algorithm they used, and not even which reference sequence, all I know is that it's human brain samples.

Any ideas how i could proceed with these files (using cufflinks for example) to compare differential gene expression? i have cufflinks already up and running.

Thanks in advance.

[nermze86]

Thank you very much, problem solved :) !

[GenoMax]

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Answer 1

[Mathias_H]

Hi, you can view the header of the BAM-files with samtools:

samtools view -H your.bam

The header tells you the sequence ID of the genome which was used for the mapping and also the alignment tool that was used.

[ATpoint]

Adding on this, typically the last lines of the header contain the commands used for alignment. In any case you can always format bam back to fastq with e.g. samtools fastq and realign / quantify against a reference of choice. That is what I would do to be sure it was done properly (not saying the company is incompetent, but simply to be sure that you can confidently stand up for the analysis).