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Forum: Bioinformatics 06-12-2013, 06:13 PM
Replies: 0
Views: 1,834
Posted By deprekate
fastq files, lowercase and base score

I am working with a bunch of fastq files from various sources. I do not know anything about the sequencing type. I have found that some have not been trimmed, and have the adapter seq in the...
Forum: Bioinformatics 10-25-2012, 04:24 PM
Replies: 0
Views: 1,390
Posted By deprekate
truncation of contig in velvet

Hi I have playing with velvet and I found this strange artifact when assembling data. When I have the following 2 sequences they get assembled into 2 contigs, both of which seem to have been clipped...
Forum: Bioinformatics 10-25-2012, 01:53 PM
Replies: 2
Views: 2,783
Posted By deprekate
Ah, yes you are correct. The length of the actual...

Ah, yes you are correct. The length of the actual sequence is >41 even though the header says length_21.
Forum: Bioinformatics 10-24-2012, 05:50 PM
Replies: 2
Views: 2,783
Posted By deprekate
meta-velvet returns nodes instead of contigs in assembly?

Hi I just started using meta-velvet to assemble a small metagenome 100k. The average length of reads are 102, with a min of 29 and a max of 227. I tried running meta-velvet with a k-mer of 21.
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