What is "M" letter in the singlets output file generated by CAP3
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7.2 years ago
seta ★ 1.7k

Hi friends,

I have made different assemblies with various k-mer, then removed redundant contigs and used CAP3 software for making meta-assembly. As you know, the CAP3 tool generated contig and singlets file as outputs. Please take a look at the following that is part of singlets file. I was wondering what is "M" letter? Since the contigs and singlets files usually will be pooled to final assembly, could you please let me know if these "M" character is problematic?

>c1
CGTACAGGGCGAGTTATTATGTTTTTGATAATCCATAAATCTTCTGTGTTCGTTTTGCAG
^MCCTGAATTTAAAACTAGAGGTTCCATCGAACCATCCAATTTTGGAAGCATGACATATTA
T^MTTCTGAAGCATCTCGTTAGAACAACATAAATCTAAATCATTAATACAAACCTCAAAGC
AT^MATGGAAATACAAACAAACACAAATAAACGCATAGGAGGAAGATACAGAATCGTTTAG
TTT^MCCTCAGCATGCCGCCCTTTGCTTCCCTTATATTATAGCTAGTTATGATGATGAAAA
GCCT^MCCTTAATCAATCTATTAAAATTATTATAAGATTTTCCTCCAATATCCGTAGTTTC
TTCAG^MCCATCTTTTTCCATTCTTGAGCCTTCTGTCTCATTTGTTTTCCCCTCTCTCCTT
CCATCA^MTTTCCTTAACAAGAGCCTCAATGTCATCACGTTTCACATCTTCATTGACTTCC
ATGCCCA^MTGCCCCAAGTTGTGCATGCATATCGACGATTCGTTTGCTGCTCAGCAAAGAA
AGGCCAAC^MAAATTACAGGAACACCACCATTTACGGTTTCAATCGTAGAATTCCACCCGC
AATGTGTTA^MAAAATAGCCCAATTGAAGGGTGAGAAAGCACTTGGTCTTGCGGACACCAA
CTTACTATTA^MACCCTCTATCCTTTATCTCTTCAAAATATTCTTGAGGCAAGATCGCAGA
ATCGTCAGTAC^MCCTCCACCACATCAGGCCTAAGAATCCATAAAAAAGGGTGTTTGCTAT
TTGCAAGACCCC^MAGGCGAATTCTTTCAGGTGCTCGTCCGACATTACAGTAATGCTACCG


Thanks a lot for your feedback.

Assembly CAP3 • 1.5k views
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How do you visualize this? I often see this when I open a windows file: https://en.wikipedia.org/wiki/Newline

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I see it in the terminal not windows.

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Type file your.cap3.file. What's the output?

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It returned

ASCII text, with CRLF, CR, LF line terminators

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CR, LF < that's your problem. cleanup your file with e.g: http://linuxcommand.org/man_pages/dos2unix1.html

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Thanks Pierre.