Thanks a lot to all for your suggestions. Finally I got the program running, by deleting the bloody white spaces in the read names and then setting -NW:mrnl=80 in MIRA, after that all worked perfectly
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If you had several lines starting GIMXFMA02G21Y1 but the descriptions were different, something strange has happened. I suspect you still have a problem in your data, and all you have done by editing the read names is avoid MIRA's sanity test without fixing the real problem.
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Originally posted by Olalla View PostSo, the read names in my fastq files appear as follows:
GIMXFMA02G21Y1 length=60 xy=2788_0299 region=2 run=R_2010_06_09_09_17_36_ that is, long names with spaces. So I think that what MIRA is doing is juts taking the first 14 characters as the read name (e.g. GIMXFMA02G21Y1),
Originally posted by Olalla View Postwhich in fact are repeated among many of the files that I do have (I have found common lines when comparing files including only these names in the lines). However, when I search for common lines in files including all information in headers (like GIMXFMA02G21Y1 length=60 xy=2788_0299 region=2 run=R_2010_06_09_09_17_36_), the output of the search is that there are no common lines between any of the files, so I think that I should first eliminate spaces, maybe replacing them by ":".
Code:grep GIMXFMA02G21Y1 your_file.fastq
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