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Hi,
I have an Illumina paired-end data set of a couple million ITS-2 sequences. I am using cd-hit-otu to do chimera checking, merging the pairs, and clustering into OTUs.
I have been getting pretty low mapping with a mean of 25% across 20 samples ranging between 1.2-53%. I have looked through the cd-hit-otu clustering folders and it seems I am loosing a lot of reads in the Assembly by looking at the link.log. Chimeras don't seem to be the problem as I am loosing very few reads here.
There doesn't seem to be a lot of information on how the reads are processed into the link.log file. When I look in the link.log file , I see that of the 573,596 cleaned reads I start with, only 180,847 are being used. This value seems to match up with the number of reads in the wrong-contigs.ids.
Does anyone have experience with cd-hit-otu or a similar problem of "missing reads?" Alternatively, can anyone provide me with more information on the link.log file or wrong-contigs.ids file in cd-hit-otu?
This product no longer seems to be supported unfortunately by the developers
Thanks in advance
I have an Illumina paired-end data set of a couple million ITS-2 sequences. I am using cd-hit-otu to do chimera checking, merging the pairs, and clustering into OTUs.
I have been getting pretty low mapping with a mean of 25% across 20 samples ranging between 1.2-53%. I have looked through the cd-hit-otu clustering folders and it seems I am loosing a lot of reads in the Assembly by looking at the link.log. Chimeras don't seem to be the problem as I am loosing very few reads here.
There doesn't seem to be a lot of information on how the reads are processed into the link.log file. When I look in the link.log file , I see that of the 573,596 cleaned reads I start with, only 180,847 are being used. This value seems to match up with the number of reads in the wrong-contigs.ids.
Does anyone have experience with cd-hit-otu or a similar problem of "missing reads?" Alternatively, can anyone provide me with more information on the link.log file or wrong-contigs.ids file in cd-hit-otu?
This product no longer seems to be supported unfortunately by the developers
Thanks in advance