which file I can use for cufflinks from the aligner STAR

Question

[yueli7]

Hello,

I have three files generated from the software of STAR after mapping: 2-pass_Aligned.out.bam, 2-pass_Aligned.sortedByCoord.out.bam, 2-pass_Aligned.toTramscriptome.out.bam.

Which one I can use for cufflilnks?

Thanks in advance!

[cpad0112]

Please post your code for generating these bams with aligner.

[WouterDeCoster]

Hi yueli7,

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Cheers,
Wouter

Answer 1

[Devon Ryan]

You'll want to use the 2-pass_Aligned.sortedByCoord.out.bam file. The transcriptome file is, as you guessed by the name alignments to a transcriptome, which is completely useless if you're trying to do de novo discovery. The 2-pass_Aligned.out.bam file is the same as the first one I mentioned, just not sorted. You can delete this and the transcriptome BAM file.

Also, use stringTie rather than cufflinks. Cufflinks should never be used for new projects.

[yueli7]

Thank you so much for your great help!