R plot doesn't seem right
JennyCNS opened this issue · 5 comments
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
Oh wait, I am running the fasta file as an input. This will not work will it?
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
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
The k-mers will be cleaner after adapter trimming.
And yes, merge (union-sum) the fastq files.