Hi,
Im new to seqanswers and bioinformatics and need a little help with Velvet. I keep getting large blocks of Ns in my PE assembly. The Ns go away when I do an assembly with just the single reads.
workfow;
~30 million PE 100bp reads
lowest average sanger quality score is 34
filter using fastx-tool kit - remove reads < 20bp in length, <30 quality over 90% of the read
also had to remove reads that failed the illumina chastity filter
remove non-PE reads after filtering and join into one file
now have ~20 million reads
velveth 31 -shortPaired
found average ins_length using velvetg: 240, sdev = 50
experimenting with parameters, I found the two genomes of interest to have coverages of 500 and 75.
I have been able to find 4-5 contigs per genome that cover nearly the entire length. The problem is that the contigs contain large blocks of Ns. For example
one assembly has 3120 contigs > 500bp in length, but there are 11634 blocks of Ns with average length of 41
in the 4 contigs that cover one of the genomes, there are 86 blocks of Ns that average 56bp in length.
How to I get rid of these Ns?
Thanks,
JT
Im new to seqanswers and bioinformatics and need a little help with Velvet. I keep getting large blocks of Ns in my PE assembly. The Ns go away when I do an assembly with just the single reads.
workfow;
~30 million PE 100bp reads
lowest average sanger quality score is 34
filter using fastx-tool kit - remove reads < 20bp in length, <30 quality over 90% of the read
also had to remove reads that failed the illumina chastity filter
remove non-PE reads after filtering and join into one file
now have ~20 million reads
velveth 31 -shortPaired
found average ins_length using velvetg: 240, sdev = 50
experimenting with parameters, I found the two genomes of interest to have coverages of 500 and 75.
I have been able to find 4-5 contigs per genome that cover nearly the entire length. The problem is that the contigs contain large blocks of Ns. For example
one assembly has 3120 contigs > 500bp in length, but there are 11634 blocks of Ns with average length of 41
in the 4 contigs that cover one of the genomes, there are 86 blocks of Ns that average 56bp in length.
How to I get rid of these Ns?
Thanks,
JT
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