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Forum: Bioinformatics 06-30-2016, 10:19 AM
Replies: 7
Views: 1,839
Posted By tonybolger
I have already given you the long answer by...

I have already given you the long answer by email, but for the benefits of the rest of the community, the key points are:


Use of compressed output is the typical bottleneck in Trimmomatic -...
Forum: Bioinformatics 11-26-2014, 06:56 AM
Replies: 189
Views: 62,149
Posted By tonybolger
It is certainly not normal - it's one of the...

It is certainly not normal - it's one of the strangest trimmomatic issue i have heard of. None the less, it should be possible to track down. Some questions:

1) Does this happen consistently on...
Forum: Bioinformatics 10-29-2014, 09:37 AM
Replies: 17
Views: 7,646
Posted By tonybolger
OK, not as much improvement as i hoped. I guess...

OK, not as much improvement as i hoped. I guess you will also need to be a bit more liberal with the SLIDINGWINDOW - maybe an average of 10 or 12, rather than 15. You could already get a major...
Forum: Bioinformatics 10-28-2014, 01:14 AM
Replies: 17
Views: 7,646
Posted By tonybolger
From the quality plots, i would guess the machine...

From the quality plots, i would guess the machine had some kind of problem during the cycle 2 and 3 in the reverse run. This could be caused by environmental problems (e.g. external vibration) or...
Forum: Bioinformatics 09-12-2014, 04:08 AM
Replies: 1
Views: 1,401
Posted By tonybolger
Yes, there is a bug with parsing the parameters...

Yes, there is a bug with parsing the parameters which only allows certain orders - all the 'option' parameters (i.e those with the minus) must currently come before non-option parameters (explicit...
Forum: Bioinformatics 09-11-2014, 02:17 AM
Replies: 2
Views: 852
Posted By tonybolger
Hi. If you see the threads created, then you...

Hi.

If you see the threads created, then you can be reasonably confident you have used the arguments correctly. The 'threads' argument (if >1) is actually the number of worker threads, so you...
Forum: Bioinformatics 08-19-2014, 12:36 AM
Replies: 189
Views: 62,149
Posted By tonybolger
Interesting - seems that file has very long lines...

Interesting - seems that file has very long lines (or is missing newlines entirely). I agree the error message should be more informative.
Forum: Bioinformatics 08-19-2014, 12:34 AM
Replies: 189
Views: 62,149
Posted By tonybolger
Good idea - it would take a bit of work, but in...

Good idea - it would take a bit of work, but in principle it can be done.
Forum: Bioinformatics 08-19-2014, 12:28 AM
Replies: 189
Views: 62,149
Posted By tonybolger
With good quality library preps, TruSeq3-PE...

With good quality library preps, TruSeq3-PE should be enough and will run much faster (since it checks only for the most common contamination scenario).

For 'strange' situations, e.g. libraries...
Forum: Bioinformatics 08-19-2014, 12:25 AM
Replies: 189
Views: 62,149
Posted By tonybolger
Most likely (especially since you are using a...

Most likely (especially since you are using a nextera prep), you have a lot of short fragments which have adapter read-through (the read length > the insert length). Since the trimmed read pairs are...
Forum: Bioinformatics 07-19-2014, 01:17 AM
Replies: 10
Views: 4,715
Posted By tonybolger
Glad you have already solved it with blakeoft's...

Glad you have already solved it with blakeoft's help.

As you see for PE mode, 6 files need to be given before the list of trimming steps (unless you use -basein/-baseout which replace 2 / 4 files...
Forum: Bioinformatics 06-25-2014, 02:58 AM
Replies: 189
Views: 62,149
Posted By tonybolger
Trimmomatic uses a slightly more complex...

Trimmomatic uses a slightly more complex strategy, so in some cases (if the quality around the trim point looks like a "U"), trimmomatic doesn't do what you expect.

Consider a typical monotonic...
Forum: Bioinformatics 06-24-2014, 05:39 AM
Replies: 189
Views: 62,149
Posted By tonybolger
This sequence looks like a TruSeq-3 adapter - if...

This sequence looks like a TruSeq-3 adapter - if so, either the TruSeq3-PE or TruSeq3-PE-2 adapter files should remove the sequencing adapters. The useful part of the reads should survive if they the...
Forum: Bioinformatics 04-16-2014, 06:54 AM
Replies: 189
Views: 62,149
Posted By tonybolger
The sliding window moves by one position each...

The sliding window moves by one position each time. So it starts with positions 1-4, if these are ok, then tries positions 2-5.

Once a 'window' falls below the required quality average, all bases...
Forum: RNA Sequencing 03-27-2014, 05:35 AM
Replies: 15
Views: 4,958
Posted By tonybolger
I've finally gotten around to testing this and it...

I've finally gotten around to testing this and it appears that the appropriate included adapter sequences (TruSeq2-PE) do a perfectly fine job with this data. Of course, it is important to actually...
Forum: RNA Sequencing 03-04-2014, 07:11 AM
Replies: 15
Views: 4,958
Posted By tonybolger
Based on relipmoc's reply, and the vintage of the...

Based on relipmoc's reply, and the vintage of the dataset, i would say these are TruSeq2 adapters (i haven't downloaded the dataset to verify) - have you tried using the TruSeq2 PE adapter file...
Forum: Bioinformatics 02-21-2014, 01:57 AM
Replies: 189
Views: 62,149
Posted By tonybolger
Generally this is caused by a partial record...

Generally this is caused by a partial record (fastq records always come in 4 line groups) at the end of the file. Blank line(s) also may also do it.
Forum: Bioinformatics 02-10-2014, 09:08 AM
Replies: 8
Views: 2,606
Posted By tonybolger
OK. I'll get a fix out for this as soon as i can...

OK. I'll get a fix out for this as soon as i can spare some time.


With read-through (due to short insert fragments), the forward adapter shows up in reverse complement in the reverse read, and...
Forum: Bioinformatics 02-10-2014, 07:35 AM
Replies: 8
Views: 2,606
Posted By tonybolger
Hi, This one is kinda embarrassing - the...

Hi,

This one is kinda embarrassing - the -baseout flag actually doesn't work the way the help suggests it should in all cases.

The 'option' arguments i.e those with a "-" must currently come...
Forum: Bioinformatics 01-13-2014, 09:22 AM
Replies: 8
Views: 4,977
Posted By tonybolger
Using phred64 on phred33 data will usually result...

Using phred64 on phred33 data will usually result in little or no output, since it lowers quality scores by 31 across the board, dropping them below any reasonable threshold. Since this is a common...
Forum: Bioinformatics 01-09-2014, 01:58 AM
Replies: 189
Views: 62,149
Posted By tonybolger
I guess some processing was already applied to...

I guess some processing was already applied to the reads, because as you say, the reads should be 150bp each. I normally recommend against using trimmed data if it all possible with Trimmomatic - it...
Forum: Bioinformatics 01-08-2014, 05:53 AM
Replies: 189
Views: 62,149
Posted By tonybolger
No problem. Can you also post the reads: ...

No problem.

Can you also post the reads:

HISEQ2000:406:H0JYCADXX:2:1101:13467:8659_/1 and HISEQ2000:406:H0JYCADXX:2:1101:13467:8659_/2

from the input files? It seems they trigger something,...
Forum: Bioinformatics 01-07-2014, 09:22 AM
Replies: 189
Views: 62,149
Posted By tonybolger
Hi, Could you tell me the command line...

Hi,

Could you tell me the command line used, including the version of trimmomatic, and also the remainder of the stack trace?

Tony.
Forum: Bioinformatics 12-14-2013, 01:21 AM
Replies: 7
Views: 8,926
Posted By tonybolger
You are correct - right now, trimmomatic doesn't...

You are correct - right now, trimmomatic doesn't perform matching with INDELs, since it is relatively rare to find them in the standard illumina datasets, and trimmomatic was very much designed to...
Forum: Bioinformatics 12-13-2013, 01:21 AM
Replies: 7
Views: 3,120
Posted By tonybolger
What library preps are you using? Adapter files...

What library preps are you using? Adapter files for the typical illumina preps (TruSeq and Nextera) are already included with recent versions of the tool.

If you have something unusual, i can...
Showing results 1 to 25 of 157

 


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