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Forum: Bioinformatics 05-19-2016, 07:09 AM
Replies: 132
Views: 49,118
Posted By mmartin
cutadapt 1.10 has just been released with support...

cutadapt 1.10 has just been released with support for "linked adapters" (5'/3' adapter pairs) and NextSeq-specific trimming, see the changelog at http://cutadapt.readthedocs.io/en/stable/changes.html...
Forum: Bioinformatics 04-22-2015, 05:52 AM
Replies: 132
Views: 49,118
Posted By mmartin
Here is the "gist" (sorry, but the indentation is...

Here is the "gist" (sorry, but the indentation is messed up):

diff --git i/cutadapt/scripts/cutadapt.py w/cutadapt/scripts/cutadapt.py
index 855721d..2eaf435 100755
---...
Forum: Bioinformatics 04-16-2015, 07:14 AM
Replies: 132
Views: 49,118
Posted By mmartin
Maybe you can use cutadaptís --info-file option:...

Maybe you can use cutadaptís --info-file option: In column 5, 6 and 7, it gives you (for each read), the sequence before the adapter, the sequence that matched the adapter and the sequence after the...
Forum: Bioinformatics 04-15-2015, 12:39 AM
Replies: 132
Views: 49,118
Posted By mmartin
Hi Pengcheng, Iíve thought about this briefly but...

Hi Pengcheng, Iíve thought about this briefly but wasnít sure how much interest would be for it and how useful that would be. Could you perhaps post this to the issue tracker...
Forum: Bioinformatics 03-14-2015, 04:01 AM
Replies: 132
Views: 49,118
Posted By mmartin
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....
Forum: Bioinformatics 02-24-2015, 03:13 AM
Replies: 132
Views: 49,118
Posted By mmartin
Great to hear you got it to work! Let me know if...

Great to hear you got it to work! Let me know if there are any further problems.
Forum: Bioinformatics 02-23-2015, 04:07 AM
Replies: 132
Views: 49,118
Posted By mmartin
In a virtual machine with Ubuntu 12.04.5, I could...

In a virtual machine with Ubuntu 12.04.5, I could reproduce the pip problem (where it says 'permission denied'). It has been fixed (https://github.com/pypa/pip/issues/440), but not in the version...
Forum: Bioinformatics 02-22-2015, 03:20 AM
Replies: 132
Views: 49,118
Posted By mmartin
I made a mistake, could you please change into...

I made a mistake, could you please change into some other directory before you run the third command, like so:
cd /; python -c 'import cutadapt; print cutadapt.__file__'


I donít have an...
Forum: Bioinformatics 02-21-2015, 09:37 AM
Replies: 132
Views: 49,118
Posted By mmartin
Very strange ... I think your friend is on the...

Very strange ... I think your friend is on the right track, but Iím guessing the problem is slightly different: The bin/cutadapt binary is actually just a small wrapper that loads the actual package...
Forum: Bioinformatics 02-20-2015, 07:35 AM
Replies: 132
Views: 49,118
Posted By mmartin
Which output did python setup.py install --user ...

Which output did python setup.py install --user
produce? Were there any error messages?
Forum: Bioinformatics 12-09-2014, 05:37 AM
Replies: 132
Views: 49,118
Posted By mmartin
Sure! IUPAC support has been on my list for a...

Sure! IUPAC support has been on my list for a while, was good to have this finally implemented.
Forum: Bioinformatics 11-25-2014, 12:48 AM
Replies: 132
Views: 49,118
Posted By mmartin
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...
Forum: Bioinformatics 11-03-2014, 08:33 AM
Replies: 132
Views: 49,118
Posted By mmartin
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...
Forum: Bioinformatics 10-06-2014, 02:15 AM
Replies: 132
Views: 49,118
Posted By mmartin
Hi, cutadapt 1.6 is now available. Here's a copy...

Hi, cutadapt 1.6 is now available. Here's a copy of the changelog.

There are no new features, but some bugs have been fixed and the documentation is now available at...
Forum: Bioinformatics 08-18-2014, 03:10 AM
Replies: 132
Views: 49,118
Posted By mmartin
There should still be eight fields, but perhaps...

There should still be eight fields, but perhaps one of the columns is empty? In that case, you'd have two consecutive tabs within a single line and it'd appear as if you only have seven fields.


...
Forum: Bioinformatics 08-05-2014, 03:49 AM
Replies: 132
Views: 49,118
Posted By mmartin
Taking your question as a motivation: I've just...

Taking your question as a motivation: I've just released cutadapt 1.5! As always, see https://code.google.com/p/cutadapt/ for the changelog and download it from PyPI...
Forum: Bioinformatics 04-23-2014, 05:26 AM
Replies: 132
Views: 49,118
Posted By mmartin
Are you talking about reads that have a length of...

Are you talking about reads that have a length of zero? This will appear as empty lines in the output file. Use cutadapt's --minimum-length option and set it to 1 or some higher value to avoid...
Forum: Bioinformatics 03-27-2014, 11:46 PM
Replies: 132
Views: 49,118
Posted By mmartin
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...
Forum: Bioinformatics 03-18-2014, 05:58 AM
Replies: 6
Views: 7,947
Posted By mmartin
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.
Forum: Bioinformatics 03-17-2014, 02:18 AM
Replies: 132
Views: 49,118
Posted By mmartin
There is a section in the README about this: ...

There is a section in the README about this:
https://github.com/marcelm/cutadapt/#illumina-truseq

In short, just run:


cutadapt -a AGATCGGAAGAGC -o trimmed.1.fastq.gz reads.1.fastq.gz...
Forum: Bioinformatics 03-13-2014, 02:08 AM
Replies: 132
Views: 49,118
Posted By mmartin
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/ .
Forum: Bioinformatics 07-02-2013, 02:09 AM
Replies: 132
Views: 49,118
Posted By mmartin
Trimming two adapters simultaneously can be...

Trimming two adapters simultaneously can be achieved by using the --times 2 option. This is not 100% the same as specifying an "adapter pair", which is not implemented, yet, see...
Forum: Bioinformatics 12-18-2012, 07:06 AM
Replies: 132
Views: 49,118
Posted By mmartin
Great, that’s the best solution I think.

Great, that’s the best solution I think.
Forum: Bioinformatics 12-18-2012, 06:51 AM
Replies: 132
Views: 49,118
Posted By mmartin
Hello Felix, Yes, having an empty...

Hello Felix,


Yes, having an empty description is allowed, too. Perhaps the message may be a bit misleading. Iíve now changed it to: ďThe second sequence description must be either empty or equal...
Forum: Bioinformatics 12-14-2012, 02:32 AM
Replies: 132
Views: 49,118
Posted By mmartin
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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