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Old 09-29-2018, 05:02 PM   #1
shandley
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Location: Saint Louis, MO

Join Date: Sep 2010
Posts: 52
Default question about dedupe renameclusters option

Hi,

How does the option renameclusters work in dedupe.sh? When I set this option to true it does not rename the contigs from 0 -> n as it does in the stats file output from csf=t. Instead, the numbers are more sporadic and over a larger range. For example, I complied the renamed contig ids with the name and size from the stats file and obtain this:

renamed_contig_id stats_file_cluster_id size
0 0 110827
1 1 13812
2 2 6812
3 3 3719
6 4 3481
9 5 2817
10 6 1880
11 7 1743
13 8 1435

Here is the command that was used to generate the clustered contig and stats file:

dedupe.sh in=input.fastq ow=t \
ac=f am=f s=4 c fo pc cc \
rnc=t sort=id \
csf=stats.txt outbest=best.fa;

How does rename cluster number? Is there anyway to make these numbers have parity with the output from csf=t?
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