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Old 02-09-2010, 06:04 PM   #1
KevinLam
Senior Member
 
Location: SEA

Join Date: Nov 2009
Posts: 203
Default solid_denovo_postprocessor.pl removes velvet contig sequence.

This question might be better directed to SOLID developers
But I have a problem where my final basespace output I have just a fasta header and no sequence. Did the solid scripts remove it because of low quality?

These are the last few steps.

velvet_0.7.55/velvetg_de ./S4output_directory/ -read_trkg yes -amos_file yes

solid_denovo_postprocessor.pl --afgfile ./S4output_directory/velvet_asm.afg --csfasta ./S4-output/colorspace_input.csfasta --run fragment --output ./sample4_input

echo 'Running denovoadp'
time denovoadp ./sample4_input 30000 > ./sample4_output


so after step 1
I get this in contigs.fa
>NODE_780_length_22_cov_13.590909
CCCCCCCCCCCCCCCCCACATGGCCGCGCCCCCCCCCCCCCC

from step 2 onwards the contig has empty sequence i.e.
>NODE_780-0
>NODE_1882-0
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