Merging several fq.gz files or R1 and R2 classes into a single one 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 _2.fq.gz
I tried doing cat *_(number).fq.gz &gt; 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.
What you did should work.  You don't need to decompress and recompress.
I'd check the files.  Were they trimmed?  Can you get the top, say 1000 lines of the merged files to work?  (You will need to decompress to count lines accurately)