Bowtie2

[lupid]

Hi to all, I'm using an old comand line that use to work for me

bowtie2 -p 3 -x Arabidopsis_thaliana.TAIR10.27.dna.toplevel.fa 60-Ab_S5_L001_R1_001.fastq > 60_ab.bam

but now generate corrupt files, what am I doing wrong??

[dpryan]

Bowtie2 doesn't produce BAM files, it produces SAM files. You likely meant:

bowtie2 -p 3 -x Arabidopsis_thaliana.TAIR10.27.dna.toplevel.fa [B]-U[/B] 60-Ab_S5_L001_R1_001.fastq | samtools view -Sbo 60_ab.bam -

I'm assuming that the index basename is correct, since otherwise you'd presumably get an error.

[GenoMax]

but now generate corrupt files, what am I doing wrong??

Can you clarify what "corrupt" means here?