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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 > 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.

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    $\begingroup$ you can use paired reads if you define the sample names in the config file. Check the sr_config_example.txt in your current installation folder. Edit the line PE= pe 500 50 with your file names, remove the JUMP line for mate pair. $\endgroup$
    – zorbax
    Nov 17, 2020 at 8:18
  • $\begingroup$ There's discussion of this topic here: biostars.org/p/81924 $\endgroup$
    – jared_mamrot
    Nov 17, 2020 at 9:00
  • $\begingroup$ Hi there, cat *_(number).fq.gz > merged(number).fq.gz should have worked. Perhaps one of the files is corrupted? You can check that using gzip -t. $\endgroup$
    – Kamil S Jaron
    Nov 18, 2020 at 12:56

1 Answer 1

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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)

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  • $\begingroup$ OP seems to have two distinct V3000* prefixes - could that be the cause for the tool to fail? $\endgroup$
    – Ram RS
    Nov 17, 2020 at 21:03
  • $\begingroup$ Who knows? I'm not familiar with the downstream tool, and no one can troubleshoot "it failed". More details are needed. $\endgroup$
    – swbarnes2
    Nov 17, 2020 at 23:26

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