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vani s kulkarni 07-10-2009 01:00 AM

velvet- stats.txt file
 
hi
I am using velvet for my solexa reads(36bp).
Can any one explain the use of stats.file, as it will be having the following information

ID, lgth, out, in, long_cov, short1_cov, short1_Ocov, short2_cov, short2_Ocov,
1 1126 0 0 0.000000 18.714032 18.714032 0.000000 0.000000
2 489 0 0 0.000000 40.832311 40.832311 0.000000 0.000000

1-what is the difference between
short1_cov, and short1_Ocov,
2-who these information is use full for selecting contigs.


Thanks

bioinfosm 07-10-2009 08:57 AM

AFAIK

In the stats file the columns refer to node id, length, number of arcs
going out, in, coverage in long reads, coverage in short reads (2 columns
for two metrics), coverage in short reads 2 (2 columns for two metrics).

allo 07-10-2009 10:56 AM

Short1_cov is the contig coverage in K-mers this count includes slightly divergent sequences
Short1_Ocov is the contig coverage in K-mers of sequences that match perfectly to each other and conform the consensus.
Both are reported in k-mers which is the hash length that you used to run velveth.

The node length gives you the size in K-mers of each contig, for example, you can sort this file by the contig size and use this info to ID the largest contig.

Torst 08-04-2009 06:58 PM

Quote:

Originally Posted by vani s kulkarni (Post 6477)
1-what is the difference between short1_cov, and short1_Ocov,

This is explained in the Manual.pdf which comes with the Velvet source code.

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