Comments on: Practical comparison of NGS adapter trimming tools https://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html Tiny bits of bioinformatics, [web-]programming etc Mon, 01 Jan 2024 17:12:20 +0000 hourly 1 https://wordpress.org/?v=3.8.27 By: Bogdanhttps://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-527317 Thu, 14 Sep 2017 20:43:19 +0000 http://bogdan.org.ua/?p=2428#comment-527317 Hi Brian,

thank you for stopping by and offering a fix! I wonder how you found this page :)

As you probably noticed, this is not a proper comparison with any degree of rigor – but rather a quick pick of “whatever seems to work”.
This is why I have not invested much effort into making BBduk run…

I’m definitely still interested in using the entire BBMAP suite – the comparison plots on sourceforge page are quite attractive.

As I’m still working with all kinds of NGS data, I’ll give BBMAP a proper try in one of my next projects.

]]> By: Brian Bushnellhttps://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-523913 Thu, 07 Sep 2017 05:19:02 +0000 http://bogdan.org.ua/?p=2428#comment-523913 Hi!

I’m not really sure why BBDuk did not work for you, but you can try this –

At the bottom of bbduk.sh is this line:
local CMD=”java -Djava.library.path=$NATIVELIBDIR $EA $z $z2 -cp $CP jgi.BBDukF $@”

Change that to:
local CMD=”java $EA $z $z2 -cp $CP jgi.BBDukF $@”

…and then it should not encounter any JNI-related problems.

]]> By: Bogdanhttps://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-522028 Tue, 29 Aug 2017 19:48:08 +0000 http://bogdan.org.ua/?p=2428#comment-522028 Hi Joyce, I haven’t added any custom adapters to the file provided with Trimmomatic, so I don’t remember the naming conventions – but they are described in the Trimmomatic manual.

]]> By: Joycehttps://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-520864 Tue, 22 Aug 2017 08:17:38 +0000 http://bogdan.org.ua/?p=2428#comment-520864 Hi,
I’m new to using trimmomatic. Been trying to get it to remove adapter sequences but it keeps missing out on the ones I specified in my adapter fasts file. Can you share with me the naming conventions needed for the trimmer to work?

Thanks!

]]> By: Bogdanhttps://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-473810 Sat, 10 Dec 2016 23:47:29 +0000 http://bogdan.org.ua/?p=2428#comment-473810 Hi, sorry for a very slow reply…
Do you still need the adapters file?
There are 2 caveats:
- I think Illumina forbids/discourages publishing adapter sequences, so I can only email those to you;
- do not assume that adapters in that file are all hand-picked and definitely correct – they were assembled from different sources and are more reminiscent of a “heap of things” than of a proper collection.

]]> By: caiohttps://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-470410 Tue, 22 Nov 2016 15:10:27 +0000 http://bogdan.org.ua/?p=2428#comment-470410 Could you share your adapters file for Trimmomatic?
Cheers

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