I have the following files:
V300066187_L4_B5RDBATtnuRAAAAA-408_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-408_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-408_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_2.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-407_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-405_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-406_1.fq.gz V300068047_L2_B5RDBATtnuRAAAAA-405_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-407_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-406_1.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_2.fq.gz V300066187_L4_B5RDBATtnuRAAAAA-405_1.fq.gz
the ending defines whether it is forward _1 or reverse _2.
I want to merge all the
_1.fq.gz files into like
Merge1_.fq.gz and the same for
I tried doing
cat *_(number).fq.gz > merged(number).fq.gz and when I used the merges for assembly with MaSurca, it didn't detect any reads and failed. I used one pair and it worked well, but the genome size was smaller than expected, real size = 2 GB, estimated = 1.8GB.
Would appreciate how to solve this issue and use all my short reads for assembly - I need to input one file for all forward reads and one file for all reverse reads.