Convert Bowtie2 alignments into Bam files.

[Milestailsprowe]

Hello I have alot of bowtie2 data in plaintext files. What would be the easist way to convert that data into .bam files for tophat/cuffdiff

[dpryan]

Samtools, but tophat uses fastq files and cuffdiff would be useless on BAM files directly from bowtie2.

[Milestailsprowe]

Samtools, but tophat uses fastq files and cuffdiff would be useless on BAM files directly from bowtie2.

So how would I prepare them for cuffdiff? Sorry if I come off uninformed I'm doing all this for my thesis project

[dpryan]

Delete them and use tophat2 directly.

[Milestailsprowe]

So I cant use anything from bowtie in tophat. The data is from bowtie2-align

[dpryan]

That's correct.

[Milestailsprowe]

That's correct.

Well ok so thats helps the situation. All data must be aligned through tophat then

[Brian Bushnell]

Well ok so thats helps the situation. All data must be aligned through tophat then

Well no, it just has to be an aligner that generates the tags needed by Cufflinks. STAR and BBMap are alternatives that generally outperform Tophat.

[dpryan]

We can probably add HISAT to that list, or so my colleagues have mentioned recently.