SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GSEA: None of the gene sets passed the size thresholds id0 Bioinformatics 3 03-08-2017 08:42 AM
100% reads passed chastity filtering? savernake Bioinformatics 6 04-29-2016 10:30 AM
how to extract passed record from a fasta.file hujiacun Bioinformatics 1 03-03-2016 01:30 AM
Ligation of Illumina adapters to custom adapters ale Sample Prep / Library Generation 2 02-29-2016 01:42 AM
Dr. Fred Sanger has passed away GenoMax General 1 11-20-2013 09:25 PM

Reply
 
Thread Tools
Old 11-29-2018, 02:35 AM   #1
tracyleighking
Junior Member
 
Location: South Africa

Join Date: Nov 2018
Posts: 1
Default Passed FastQC - but adapters still present?

Hi there - I am brand new to both Bioinformatics and this forum so I hope I'm posting in the right place; and that my questions make sense!

I have Enterococcus isolates that were sequenced using a MiSeq sequencer, and currently I've been playing around with the raw fastq files in UGENE, CGE tools, and most recently the NCBI Prokaryotic Annotation Pipeline. My aim is to check out the resistance genes, sequence types, phylogeny etc of the isolates.

I used FASTQC to check the quality of one of my isolates, then the SPAdes assembler on CGE. I then submitted to NCBI PGAP. I got an error message back though saying contam - i.e. an adapter.

I'm not sure how to proceed. I know there are (tons of) adapter trimming programs - my issue is I'm exclusively Windows based at the moment - I'm really trying to learn Unix/command line but I'm struggling with this.

Anyone have any tips; either re Windows/web based adapter trimming and/or (easy!) command line software?

Thanks so much!
tracyleighking is offline   Reply With Quote
Old 11-30-2018, 06:57 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,813
Default

You can use bbduk from BBMap suite to remove adapter contamination. BBMap suite is pure java so it will work on windows as well.
GenoMax is offline   Reply With Quote
Reply

Tags
adapter trimming, pgap, prokaryotes, windows

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:33 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO