R plot doesn't seem right

[JennyCNS]

Hello,

I am running the following script

estimate best k

sh $MERQURY/best_k.sh 1089729222

19.9928 so 20

# 1. Build meryl dbs
meryl k=20 count fEpiCoi_cnag1_curated_primary.no_mt.fa output hamour-genome-job.meryl threads=9 memory=130

#2. merge output
meryl union-sum ./hamour.meryl output hamour.meryl

$MERQURY/merqury.sh hamour.meryl fEpiCoi_cnag1_curated_primary.no_mt.fa test1

when I merge the files together I still have a lot of files in the folder,

and my plots look like this

Is there any way you can help me with figure out what is wrong with the analysis?

Thank you,

Jennifer

[JennyCNS]

Oh wait, I am running the fasta file as an input. This will not work will it?

[arangrhie]

Hello, in this step:

 # 1. Build meryl dbs

You need to use the reads (fq or fa) not the assembly.

Also you could skip

#2. merge output
meryl union-sum ./hamour.meryl output hamour.meryl

If there is only one meryl file to merge :)

Best, Arang

[JennyCNS]

Hi, I am really sorry for being a pain again but should I merge my forward reverse fastq files for the analysis or just trim the adaptors?

Thank you

[arangrhie]

The k-mers will be cleaner after adapter trimming. And yes, merge (union-sum) the fastq files.

[arangrhie]

@JennyCNS feel free to re-open if you need more help! I've noticed meryl v1.4 had an issue in meryl-lookup, so please use v1.4.1 release instead..!!