Question: Masking Uncovered Segments Of Assembled Contig
3
gravatar for 2184687-1231-83-
8.6 years ago by
2184687-1231-83-4.9k wrote:

Hi,

I've got contigs assembled from a read set, and I want a simple tool that, for a subset of the reads, will map again to the contig and mask with NNNs those parts of the contig that are not covered by the read subset.

What would be a good tool for that?

I've been told I should script around pileup, but I refuse to think there isn't an easier way of doing it already.

Cheers

assembly reference • 1.3k views
ADD COMMENTlink written 8.6 years ago by 2184687-1231-83-4.9k

Hi @Avilella. What kind of format are the data in? .fasta? .ace? Are there low quality ends on your assembled sequences (such as would be described in an .ace file) that should not be included in your mapped region of the contigs? Would you accept a Python solution using Biopython or do you absolutely want an already made program? Cheers!

ADD REPLYlink written 8.6 years ago by Eric Normandeau10k
3
gravatar for Pierre Lindenbaum
8.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

maskFastaFromBed from the bedtools? See here

ADD COMMENTlink modified 5 months ago by RamRS20k • written 8.6 years ago by Pierre Lindenbaum116k
0
gravatar for 2184687-1231-83-
8.6 years ago by
2184687-1231-83-4.9k wrote:

Answering my own question, I actually ended up using maq easyrun and using the consensus sequence.

perl ~/src/maq/maq-0.7.1/scripts/maq.pl easyrun -d outdir 327.columbus/contigs.fa 286557.reads
ADD COMMENTlink modified 5 months ago by RamRS20k • written 8.6 years ago by 2184687-1231-83-4.9k
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