Forum: Bioinformatics
06-30-2016, 11:19 AM
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Replies: 7
Views: 2,665
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 -...
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Forum: Bioinformatics
11-26-2014, 07:56 AM
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Replies: 189
Views: 76,124
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...
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Forum: Bioinformatics
10-29-2014, 10:37 AM
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Replies: 17
Views: 10,012
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Forum: Bioinformatics
10-28-2014, 02:14 AM
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Replies: 17
Views: 10,012
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Forum: Bioinformatics
09-12-2014, 05:08 AM
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Replies: 1
Views: 1,872
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...
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Forum: Bioinformatics
09-11-2014, 03:17 AM
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Replies: 2
Views: 1,131
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...
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Forum: Bioinformatics
08-19-2014, 01:36 AM
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Replies: 189
Views: 76,124
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Forum: Bioinformatics
08-19-2014, 01:34 AM
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Replies: 189
Views: 76,124
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Forum: Bioinformatics
08-19-2014, 01:28 AM
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Replies: 189
Views: 76,124
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...
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Forum: Bioinformatics
08-19-2014, 01:25 AM
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Replies: 189
Views: 76,124
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...
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Forum: Bioinformatics
07-19-2014, 02:17 AM
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Replies: 10
Views: 7,326
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Forum: Bioinformatics
06-25-2014, 03:58 AM
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Replies: 189
Views: 76,124
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...
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Forum: Bioinformatics
06-24-2014, 06:39 AM
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Replies: 189
Views: 76,124
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Forum: Bioinformatics
04-16-2014, 07:54 AM
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Replies: 189
Views: 76,124
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...
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Forum: RNA Sequencing
03-27-2014, 06:35 AM
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Replies: 15
Views: 5,870
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Forum: RNA Sequencing
03-04-2014, 08:11 AM
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Replies: 15
Views: 5,870
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Forum: Bioinformatics
02-21-2014, 02:57 AM
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Replies: 189
Views: 76,124
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Forum: Bioinformatics
02-10-2014, 10:08 AM
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Replies: 8
Views: 3,327
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Forum: Bioinformatics
02-10-2014, 08:35 AM
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Replies: 8
Views: 3,327
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...
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Forum: Bioinformatics
01-13-2014, 10:22 AM
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Replies: 8
Views: 6,890
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Forum: Bioinformatics
01-09-2014, 02:58 AM
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Replies: 189
Views: 76,124
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...
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Forum: Bioinformatics
01-08-2014, 06:53 AM
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Replies: 189
Views: 76,124
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,...
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Forum: Bioinformatics
01-07-2014, 10:22 AM
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Replies: 189
Views: 76,124
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Forum: Bioinformatics
12-14-2013, 02:21 AM
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Replies: 7
Views: 10,744
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Forum: Bioinformatics
12-13-2013, 02:21 AM
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Replies: 7
Views: 3,783
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