View Single Post
Old 01-19-2018, 12:06 PM   #283
catagui
Junior Member
 
Location: Florida, USA

Join Date: Mar 2017
Posts: 3
Default

Hi I would like to use bbduk to filter the reads that map to a genome. I have 48 pair samples and want to make sure I understand how to input the file.
My sample are are Pair end and are labeled as F and R (plus _1 and _2).
Should I put them all after in= ? or use in2= for the reverse? Does interleave means that I put each pair together?
eg. in= S1_F_paired_1.fq,S1_R_paired_2.fq,S10_F_paired_1.fq,S10_R_paired_2.fq...

I have them as two separate lines at the moment:
S1_F_paired_1.fq,S10_F_paired_1.fq,S11_F_paired_1.fq,S12_F_paired_1.fq,S13_F_paired_1.fq..
S1_R_paired_2.fq,S10_R_paired_2.fq,S11_R_paired_2.fq,S12_R_paired_2.fq,S13_R_paired_2.fq..

Thanks,

Catalina
catagui is offline   Reply With Quote