Runs of N's in contigs
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milner...@scigenom.com
Apr 22, 2014, 5:08:53 AM4/22/14
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Dear ABySS-users,
We
assembled bacterial contigs and submitted to NCBI. Some of the contigs
have runs of N's in it. They have the following queries regarding the
same. Please help us to resolve the queries.
[A] Did the assembly program combine the sequences into scaffolds using runs of N's to represent gaps between ordered and oriented contiguous sequences? Alternatively, did you randomly merge the sequences into a single sequence (for example, may be you just linked the sequences together by size without using an assembly program)?
[B] Does every N in your sequence represent a gap? Alternatively, does your sequence include single or short runs of N's that represent ambiguous base calls? If not every N is a gap, what is the minimum number of N's that represent a gap? In order for us to add the assembly_gap features for you, we need to input a minimum gap size to tell our software which N's to convert.
[C] In each gap, does the number of N's represent the estimated gap size? Alternatively, are all or some of the gap sizes unknown? If there are unknown gaps, please specify which ones. For example, are all of the gaps of 100 N's unknown length?
With regards,[A] Did the assembly program combine the sequences into scaffolds using runs of N's to represent gaps between ordered and oriented contiguous sequences? Alternatively, did you randomly merge the sequences into a single sequence (for example, may be you just linked the sequences together by size without using an assembly program)?
[B] Does every N in your sequence represent a gap? Alternatively, does your sequence include single or short runs of N's that represent ambiguous base calls? If not every N is a gap, what is the minimum number of N's that represent a gap? In order for us to add the assembly_gap features for you, we need to input a minimum gap size to tell our software which N's to convert.
[C] In each gap, does the number of N's represent the estimated gap size? Alternatively, are all or some of the gap sizes unknown? If there are unknown gaps, please specify which ones. For example, are all of the gaps of 100 N's unknown length?
M. Milner Kumar,
Dinesh Reghunathan
May 3, 2014, 7:51:12 AM5/3/14
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I am trying to remove N from my contigs.fa file, I am currently using abyss 1.3.7 and to remove N i have usied the following script "abyss-fatoagp -f <split_contigs_file> -s <minimum_contig_length> *-scaffolds.fa >scaffolds.agp" but it seems the agp file is repeatedly coming as a blank file. and the program is not showing any error also. Kindly give any valuable suggestions
Dinesh Reghunathan
May 5, 2014, 12:09:38 AM5/5/14
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I am trying to remove N from my contigs.fa file, I am currently using abyss 1.3.7 and to remove N i have usied the following script "abyss-fatoagp -f <split_contigs_file> -s <minimum_contig_length> *-scaffolds.fa >scaffolds.agp" but it seems the agp file is repeatedly coming as a blank file. and the program is not showing any error also. Kindly give any valuable suggestions
Regards
Dinesh
Dinesh
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