Question: genomescope profile failed to converge
0
gravatar for StudentBio
12 months ago by
StudentBio0
StudentBio0 wrote:

hello the community,

to estimate the characteristics of my genome I used GenomeScope, as a result I got an error like GenomeScope profile failed to converge and depending on what i found the problem is because low coverage or low quality reads ....so please if anyone can help me to solve this this my fastqc report after trimming enter image description here

fastqc report after trimming with sickle

jellyfish k-mers genomescope • 716 views
ADD COMMENTlink modified 12 months ago by lieven.sterck5.5k • written 12 months ago by StudentBio0

I assume you did use the jellyfish tool to count the kmer? If oyu used any other software (ntCard ?) you need to modify the input count table before uploading it to genomescope

It might also depend on the kmer size you used, so try to play around with that one a bit and see if it gets better?

ADD REPLYlink modified 12 months ago • written 12 months ago by lieven.sterck5.5k

I removed the -C option from jellyfish and it worked thank you very much jellyfish count -m 17 -s 1000000000 -t 10 /home/vshare/bowtie2/trimmed.fastq -o reads2.jf

ADD REPLYlink written 12 months ago by StudentBio0
1
gravatar for lieven.sterck
12 months ago by
lieven.sterck5.5k
VIB, Ghent, Belgium
lieven.sterck5.5k wrote:

I had this myself as well on several occasions. it's often due to the fact that you have too low coverage of data and that you thus not see the typical peaks appearing (yet at that coverage) . You should anyhow get a graph, no? on that you will see that you're lacking the peak the software needs to do it's calculations and thus not converges.

EDIT: is also should not have anything to do with FastQC processing, it should work as good (or bad) on trimmed or untrimmed data

ADD COMMENTlink modified 12 months ago • written 12 months ago by lieven.sterck5.5k

Same for me, lack of coverage so no peak, I've never seen anything else myself.

There's an unlikely chance that it's a highly fragmented genome, see Suppl. Figure 3 in 'The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes'. But again, unlikely.

ADD REPLYlink written 12 months ago by Philipp Bayer6.3k

small world ... paper of good colleagues of me :)

ADD REPLYlink written 12 months ago by lieven.sterck5.5k

Tell them 'congratulations' from me, it's a really cool paper!

ADD REPLYlink written 12 months ago by Philipp Bayer6.3k

thanks of you all i can resolve it removing the -C option from jellyfish and it worked jellyfish count -m 17 -s 1000000000 -t 10 /home/vshare/bowtie2/trimmed.fastq -o reads2.jf

ADD REPLYlink written 12 months ago by StudentBio0
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