hisat2 - clean paired data

Question

[lrg4n]

Hi - I've been using hisat2 with success with my data, but have turned to previously published RNAseq data to analyze and confirm their results. I've cleaned the two paired Illumina (HiSeq 2000) sequence reads that I've downloaded from ENA with trimmomatic, but when I use them to align to hg19, hisat2 does not recognize the files as paired reads. I've checked the files to ensure that they are paired ( HWI-ST423:1:22:1478:2080:/1 and HWI-ST423:1:22:1407:2122:/2). Any thoughts? I'm still new at this, but I'm getting much more comfortable! Thank you in advance. Laurie

Answer 1

[h.mon]

Are HWI-ST423:1:22:1478:2080:/1 and HWI-ST423:1:22:1407:2122:/2 the first reads from R1 (forward) and R2 (reverse) files? If yes, your file is not paired paired reads would be like HWI-ST423:1:22:1478:2080:/1 and HWI-ST423:1:22:1478:2080:/2.

[lrg4n]

Got it! Thank you. I appreciate your help.