Forum: Bioinformatics
05-19-2016, 08:09 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
04-22-2015, 06:52 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
04-16-2015, 08:14 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
04-15-2015, 01:39 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
03-14-2015, 05:01 AM
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Replies: 132
Views: 54,771
cutadapt 1.8
Hi, cutadapt 1.8 has been released. It (finally) comes with proper paired-end support (no need to run cutadapt twice), quality-trimming of 5' ends and filtering of reads that have too many N bases....
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Forum: Bioinformatics
02-24-2015, 04:13 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
02-23-2015, 05:07 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
02-22-2015, 04:20 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
02-21-2015, 10:37 AM
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Replies: 132
Views: 54,771
Very strange ... I think your friend is on the...
Very strange ... I think your friend is on the right track, but I’m guessing the problem is slightly different: The bin/cutadapt binary is actually just a small wrapper that loads the actual package...
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Forum: Bioinformatics
02-20-2015, 08:35 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
12-09-2014, 06:37 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
11-25-2014, 01:48 AM
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Replies: 132
Views: 54,771
Cutadapt 1.7 released
Hi there, cutadapt 1.7 is now available. Here are the most important new features:
Support for IUPAC characters
Demultiplexing of FASTQ files
Added an "anchored 3' adapter" type
And of...
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Forum: Bioinformatics
11-03-2014, 09:33 AM
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Replies: 132
Views: 54,771
Hi Francy,
I think Phil gave the correct...
Hi Francy,
I think Phil gave the correct answer. It seems the adapter sequence is compatible with Illumina’s adapter (it probably has to be for it to work), and so you need to trim the same...
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Forum: Bioinformatics
10-06-2014, 03:15 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
08-18-2014, 04:10 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
08-05-2014, 04:49 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
04-23-2014, 06:26 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
03-28-2014, 12:46 AM
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Replies: 132
Views: 54,771
Cutadapt removes only one adapter per read, so...
Cutadapt removes only one adapter per read, so you need to run it twice with each adapter or specify the option --times=2. Also, you should use specify the 3' adapter starting with a "^" like so: -g...
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Forum: Bioinformatics
03-18-2014, 06:58 AM
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Replies: 6
Views: 8,864
Relevant for me was lh3's comment in another...
Relevant for me was lh3's comment in another thread: (http://seqanswers.com/forums/archive/index.php/t-9717.html): Use the -A option with mpileup in order to include non-properly-paired reads.
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Forum: Bioinformatics
03-17-2014, 03:18 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
03-13-2014, 03:08 AM
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Replies: 132
Views: 54,771
Cutadapt 1.4 released
Hi, I've just released cutadapt 1.4, which comes with some speed improvements, bug fixes and also new features. See the detailed changelog at http://code.google.com/p/cutadapt/ .
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Forum: Bioinformatics
07-02-2013, 03:09 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
12-18-2012, 08:06 AM
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Replies: 132
Views: 54,771
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Forum: Bioinformatics
12-18-2012, 07:51 AM
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Replies: 132
Views: 54,771
Hello Felix,
Yes, having an empty...
Hello Felix,
Yes, having an empty description is allowed, too. Perhaps the message may be a bit misleading. I’ve now changed it to: “The second sequence description must be either empty or equal...
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Forum: Bioinformatics
12-14-2012, 03:32 AM
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Replies: 132
Views: 54,771
3' ends that have a bad quality can be removed...
3' ends that have a bad quality can be removed with the -q option, but that does not remove a fixed number of bases (see the --help) and also does not work for 5' ends. In any case, cutadapt always...
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