Forum: Bioinformatics
08-25-2015, 07:29 AM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
08-24-2015, 06:39 AM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
08-12-2015, 06:11 PM
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Replies: 10
Views: 1,510
try skewer
Another option is skewer (http://sourceforge.net/projects/skewer). Good luck!
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Forum: Bioinformatics
08-04-2015, 07:52 PM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
07-25-2015, 09:05 AM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
05-01-2015, 02:42 AM
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Replies: 5
Views: 2,529
use skewer
Hi ddelalca,
You may use skewer (https://sourceforge.net/projects/skewer/) for this purpose. An example command line is as follows:
skewer -x V3-forward.txt -y V4-reverse.txt --mode ap -t 4...
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Forum: Bioinformatics
11-13-2014, 08:58 AM
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Replies: 62
Views: 29,036
Yes, you are right!:)
BTW: I found that most...
Yes, you are right!:)
BTW: I found that most of the users just use skewer for preprocessing Long Mate Pair reads. It seems that few people noticed the competence of skewer to trim adapters from...
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Forum: Bioinformatics
10-24-2014, 01:57 AM
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Replies: 62
Views: 29,036
Hi travc,
The best scenario of using...
Hi travc,
The best scenario of using skewer is for pre-processing raw data, especially for pre-processing those data of complex libraries such as Nextera LMPs. To make things clearer, I suggest...
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Forum: Bioinformatics
10-22-2014, 11:08 PM
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Replies: 17
Views: 10,197
hi BADE,
You may try skewer ...
hi BADE,
You may try skewer (http://sourceforge.net/projects/skewer/) for preprocessing your data. It's demonstrated to produce better input for downstream analysis of RNA-Seq data. It's easy to...
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Forum: Bioinformatics
10-03-2014, 09:51 PM
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Replies: 3
Views: 2,453
try skewer
Hi Palgrave,
From the pdf (http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-customer-sequence-letter.pdf) file...
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Forum: Illumina/Solexa
09-29-2014, 10:43 AM
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Replies: 6
Views: 1,883
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Forum: Illumina/Solexa
09-29-2014, 10:29 AM
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Replies: 145
Views: 322,354
Skewer supports demultiplexing amplicon pairs
Recently we indexed 6 amplicon libraries and sequenced them in a 2 x 300bp MiSeq run. Each of these 6 amplicon libraries was also a mixed library which contains about 60 samples barcoded by different...
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Forum: Bioinformatics
09-29-2014, 09:55 AM
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Replies: 62
Views: 29,036
Corrected adapter sequences
The following adapter sequences are provided for your convenience:
>TruSeq read 1 universal adapter
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG
>TruSeq read 2 adapter...
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Forum: Bioinformatics
09-29-2014, 09:48 AM
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Replies: 62
Views: 29,036
Then I used your software as:
After...
Then I used your software as:
After that I used bowtie to see how the alignment will go but;
so did I used the parameter in wrong way? or what I shall add or change?[/QUOTE]
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Forum: Bioinformatics
09-27-2014, 06:55 AM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
08-24-2014, 03:43 PM
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Replies: 62
Views: 29,036
Thanks for this question! Now the result files...
Thanks for this question! Now the result files can be redirected into a directory using -o. The difference is that a directory name must end with a slash '/'. I'll release the updated version soon.
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Forum: Bioinformatics
08-24-2014, 03:04 PM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
08-07-2014, 06:37 PM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
08-04-2014, 11:17 PM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
06-13-2014, 09:56 AM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
06-13-2014, 09:47 AM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
06-08-2014, 10:51 AM
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Replies: 62
Views: 29,036
Hi blsfoxfox,
Thank you very much for...
Hi blsfoxfox,
Thank you very much for your feedback! The name of the parameter is misleading. Its actual meaning is the maximum equivalent read length. For example, if the length of trimmed...
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Forum: Bioinformatics
06-05-2014, 08:01 AM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
06-04-2014, 06:35 PM
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Replies: 62
Views: 29,036
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Forum: Bioinformatics
06-04-2014, 06:32 PM
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Replies: 62
Views: 29,036
Hi Luc,
Thank you for your question! My...
Hi Luc,
Thank you for your question! My answer goes as follows:
The length threshold -k does not influence the trimming result of paired-end data. Other length thresholds such as -l and -L...
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