Question: What is "M" letter in the singlets output file generated by CAP3
0
gravatar for seta
3.2 years ago by
seta1.1k
Sweden
seta1.1k wrote:

Hi freinds,

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  alot for your feedback.

cap3 contig assembly singlets • 817 views
ADD COMMENTlink written 3.2 years ago by seta1.1k

how do you visualize this ? I often see this when I open a windows file : https://en.wikipedia.org/wiki/Newline

ADD REPLYlink written 3.2 years ago by Pierre Lindenbaum115k

I see it in the terminal not windows.

 

ADD REPLYlink written 3.2 years ago by seta1.1k

type

file  your.cap3.file

 

 what's the output ?

ADD REPLYlink written 3.2 years ago by Pierre Lindenbaum115k

It returned  ASCII text, with CRLF, CR, LF line terminators. 

ADD REPLYlink written 3.2 years ago by seta1.1k

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

ADD REPLYlink written 3.2 years ago by Pierre Lindenbaum115k

Thanks Pierre.

ADD REPLYlink written 3.2 years ago by seta1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1063 users visited in the last hour