Hi all,
I have some metagenomics reads, I trim them with trimmomatic and remove adapters using some illumina adapters library I found on the internet.
Then I look at them in Fastqc and it says that "adapter content" is very bad and "kmer content" is very bad as well (which must mean that there are indeed lots of adapters), the question is -- how do I remove these adapters?
How does Fastqc know they are there? Is it using some adapter database? If so, I would like to use that database to remove them! Where is the Fullest Possible Illumina Adapters Library (because the one I'm using right now isn't full enough)? Or Fastqc is mistaking?
•
written
by
hed.robin •
1 answer
using some illumina adapters library I found on the internet
And did you verify that those are the same ones that are used in the sequencing reaction that was performed to realize your data? I've been using trimmomatic a lot and never had problems, I guess that you might have specified the wrong adapters!
Check your sequencing information: which Illumina technology was used?
Then, search for it here: http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf
You'll find the right sequences. ;)
Log in to answer this question.
-
Are truseq adapter sequences picked up by FASTQC?
written by bioinfo •
-
How to find out what adapters to remove after FastQC of RNAseq data?
written by ella •
-
No trimming of reverse reads using Trimmomatic-0.39
written by hgal4248 •
-
ATAC-Seq kmer removal
written by elenichri •
-
kmer content changes after trimming and removing adapters from reads
written by serpalma.v •
-
Which truseq trimmomatic adapters file to use when removing truseq adapters?
written by salamandra
-
Issues with Illumina Universal Adapters
written by williamsbrian5064
-
Isn't fastq file header suppose to have barcode sequence?
written by salamandra
-
adapter trimming PE RNA reads
written by rahmati.razieh83 •
-
trimming PE RNA Reads
written by rahmati.razieh83 •
there is a nice tool called BBmap from which you can use
bbduck.shthat contains what you needand it would be nice if you can support us with the tool, command and parameters that would make the answer more clear
Program is actually called
bbduk.sh. BBMap suite also includes aadapters.fafile (in "resources" directory in source) that includes common commercial adapter sequences so you don't need to search for dodgy sources on the net or type the sequences in by hand.according to the author documentation he wrote
which will take you to the BBmap web (maybe I am mistaken about it)
dukstands fordecontamination using k-mers. You wrotebbduck.shin the post above (which is a mistake I sometimes do). I was just correcting the program name. All BBTools are included in a single download.you are totally right I did not see this C (my bad :) )
@hed.robin Yes. FastQC uses a database kept inside Configuration directory. Look for files: adapter_list.txt and contaminant_list.txt