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Forum: Bioinformatics 08-25-2015, 06:29 AM
Replies: 62
Views: 28,177
Posted By relipmoc
It runs well in my server. Could you please send...

It runs well in my server. Could you please send the small_test.fastq to xxx@xxxxxx (see the skewer paper) Thank you!

BTW: are you sure that you used version 0.1.127? This version fixed some bugs...
Forum: Bioinformatics 08-24-2015, 05:39 AM
Replies: 62
Views: 28,177
Posted By relipmoc
Sorry for the inconvenience brought to you! Could...

Sorry for the inconvenience brought to you! Could you please send an email to me about the command you used as well as a minimum dataset that can cause the segmentation fault?
Forum: Bioinformatics 08-12-2015, 05:11 PM
Replies: 10
Views: 1,437
Posted By relipmoc
try skewer

Another option is skewer (http://sourceforge.net/projects/skewer). Good luck!
Forum: Bioinformatics 08-04-2015, 06:52 PM
Replies: 62
Views: 28,177
Posted By relipmoc
Hi marghi, Please download version 0.1.127...

Hi marghi,
Please download version 0.1.127 and run the following command:
$ skewer -m ap --barcode -x GAT -r 0 small_test.fastq -o GAT_small_test
You will get what you want.
Forum: Bioinformatics 07-25-2015, 08:05 AM
Replies: 62
Views: 28,177
Posted By relipmoc
Hi marghi, Thank you for your feedback!...

Hi marghi,
Thank you for your feedback! This use case was not considered by skewer. We'll add the codes for processing it in the future.
Forum: Bioinformatics 05-01-2015, 01:42 AM
Replies: 5
Views: 2,421
Posted By relipmoc
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...
Forum: Bioinformatics 11-13-2014, 07:58 AM
Replies: 62
Views: 28,177
Posted By relipmoc
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...
Forum: Bioinformatics 10-24-2014, 12:57 AM
Replies: 62
Views: 28,177
Posted By relipmoc
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...
Forum: Bioinformatics 10-22-2014, 10:08 PM
Replies: 17
Views: 9,673
Posted By relipmoc
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...
Forum: Bioinformatics 10-03-2014, 08:51 PM
Replies: 3
Views: 2,325
Posted By relipmoc
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...
Forum: Illumina/Solexa 09-29-2014, 09:43 AM
Replies: 6
Views: 1,796
Posted By relipmoc
If you have raw fastq files where all the reads...

If you have raw fastq files where all the reads are of the same length, you may use skewer for adapter trimming.

See http://www.biomedcentral.com/1471-2105/15/182/ for your reference.
Forum: Illumina/Solexa 09-29-2014, 09:29 AM
Replies: 145
Views: 319,314
Posted By relipmoc
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...
Forum: Bioinformatics 09-29-2014, 08:55 AM
Replies: 62
Views: 28,177
Posted By relipmoc
Corrected adapter sequences

The following adapter sequences are provided for your convenience:

>TruSeq read 1 universal adapter
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG

>TruSeq read 2 adapter...
Forum: Bioinformatics 09-29-2014, 08:48 AM
Replies: 62
Views: 28,177
Posted By relipmoc
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]
Forum: Bioinformatics 09-27-2014, 05:55 AM
Replies: 62
Views: 28,177
Posted By relipmoc
Now skewer provides an option for it. Please...

Now skewer provides an option for it. Please download the updated version from http://sourceforge.net/projects/skewer (https://sourceforge.net/projects/skewer/files/Binaries/).
Forum: Bioinformatics 08-24-2014, 02:43 PM
Replies: 62
Views: 28,177
Posted By relipmoc
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.
Forum: Bioinformatics 08-24-2014, 02:04 PM
Replies: 62
Views: 28,177
Posted By relipmoc
Sorry for not giving you a quick reply! In fact,...

Sorry for not giving you a quick reply! In fact, JA (Junction Adapter) has nothing to do with barcode dispatch. JA can be regarded as a marker for correctly constructed LMP pairs. However, JA may be...
Forum: Bioinformatics 08-07-2014, 05:37 PM
Replies: 62
Views: 28,177
Posted By relipmoc
Fragments equal to or shorter than 300 bp without...

Fragments equal to or shorter than 300 bp without JA belong to this group.


Fragments longer than 300 bp and none of the two paired reads having JA detected belong to this group.

These...
Forum: Bioinformatics 08-04-2014, 10:17 PM
Replies: 62
Views: 28,177
Posted By relipmoc
"SE trimming" means removing junction adapter and...

"SE trimming" means removing junction adapter and its following sequence at the 3' end.


(A) There may be several candidate overlap sites, the best overlap is selected according to the scoring...
Forum: Bioinformatics 06-13-2014, 08:56 AM
Replies: 62
Views: 28,177
Posted By relipmoc
skewer has been accepted as a methodology paper in BMC Bioinformatics

If you find skewer is useful for your study, please kindly cite it in your paper. Thank you!

BMC Bioinformatics.2014, 15:182
DOI: 10.1186/1471-2105-15-182
URL:...
Forum: Bioinformatics 06-13-2014, 08:47 AM
Replies: 62
Views: 28,177
Posted By relipmoc
We will add a parameter for clipping bases in the...

We will add a parameter for clipping bases in the future versions.


Good question! For Nextera long mate-pair (LMP) reads, skewer first treats them as normal paired-end (PE) reads and trims...
Forum: Bioinformatics 06-08-2014, 09:51 AM
Replies: 62
Views: 28,177
Posted By relipmoc
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...
Forum: Bioinformatics 06-05-2014, 07:01 AM
Replies: 62
Views: 28,177
Posted By relipmoc
Could you show us the problematic PE reads in...

Could you show us the problematic PE reads in FASTQ format? So that I can figure out what's wrong with the program.



The answer is NO.
Forum: Bioinformatics 06-04-2014, 05:35 PM
Replies: 62
Views: 28,177
Posted By relipmoc
Smile Hi roryk, thank you for your feedback!

Hi roryk, thank you for your feedback!
Forum: Bioinformatics 06-04-2014, 05:32 PM
Replies: 62
Views: 28,177
Posted By relipmoc
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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