Forum: Bioinformatics
05-30-2017, 02:22 PM
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Replies: 5
Views: 5,625
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Forum: Bioinformatics
12-06-2016, 10:58 AM
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Replies: 13
Views: 2,426
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Forum: Bioinformatics
12-06-2016, 10:17 AM
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Replies: 13
Views: 2,426
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Forum: Bioinformatics
10-31-2014, 04:26 AM
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Replies: 17
Views: 2,298
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Forum: Bioinformatics
10-30-2014, 10:03 AM
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Replies: 17
Views: 2,298
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Forum: Bioinformatics
10-30-2014, 09:58 AM
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Replies: 5
Views: 2,001
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Forum: Bioinformatics
10-29-2014, 08:25 AM
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Replies: 17
Views: 2,298
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Forum: Bioinformatics
10-28-2014, 06:25 AM
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Replies: 17
Views: 2,298
I'm not sure how to answer. Your read names...
I'm not sure how to answer. Your read names should not have any overlaps. How did you generate your fastq files? I tend to use mira's sff_extract. But there are lots of good sff extractors out...
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Forum: Bioinformatics
10-27-2014, 10:01 AM
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Replies: 17
Views: 2,298
I'm wondering if the trimming process may not...
I'm wondering if the trimming process may not have clipped the read names - are you able to check that?
Also, mira works better if you do NOT preprocess your data - as mira will trim internally...
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Forum: Bioinformatics
10-09-2014, 01:45 PM
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Replies: 2
Views: 1,085
You also, unless you really know what you are...
You also, unless you really know what you are doing, should consider not using sequence reads without quality data with Mira, unless you have chopped up a finished sequence and are doing something...
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Forum: Bioinformatics
09-19-2014, 07:01 AM
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Replies: 7
Views: 2,793
There are several approaches of varying...
There are several approaches of varying complexity and cost:
The easiest in my recent experience, is to get PacBio sequencing done. With the illumina reads mapped to a PacBio assembly, you can...
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Forum: Bioinformatics
07-21-2014, 01:12 PM
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Replies: 12
Views: 4,010
I recommend two things:
1. Try the mira list...
I recommend two things:
1. Try the mira list where they are very helpful: http://www.freelists.org/list/mira_talk
2. Ask your PacBio sequencing provider for the metadata.xml, bas.h5 and bax.h5...
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Forum: Bioinformatics
07-11-2014, 12:00 PM
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Replies: 13
Views: 3,341
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Forum: Bioinformatics
07-07-2014, 04:13 PM
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Replies: 13
Views: 3,341
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Forum: Bioinformatics
07-02-2014, 07:53 AM
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Replies: 2
Views: 2,822
Maybe "bamtools" could help...
Maybe "bamtools" could help (https://github.com/pezmaster31/bamtools)
e.g. $ bamtools stats -n YourFile.bam
**********************************************
Stats for BAM file(s):...
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Forum: Bioinformatics
03-05-2014, 06:10 PM
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Replies: 3
Views: 1,282
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Forum: Bioinformatics
03-01-2014, 02:05 PM
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Replies: 6
Views: 1,477
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Forum: Bioinformatics
02-07-2014, 02:47 PM
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Replies: 8
Views: 1,874
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Forum: Bioinformatics
01-31-2014, 03:44 AM
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Replies: 2
Views: 2,193
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Forum: Bioinformatics
12-11-2013, 10:58 AM
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Replies: 2
Views: 1,826
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Forum: Bioinformatics
10-27-2013, 07:12 AM
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Replies: 17
Views: 4,567
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Forum: Bioinformatics
08-13-2013, 10:16 AM
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Replies: 9
Views: 4,369
Try this:...
Try this: https://code.google.com/p/nash-bioinformatics-codelets/downloads/detail?name=subset_fasta.pl&can=2&q=
Hopefully it will do the job you need.
J
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Forum: Bioinformatics
05-10-2013, 03:35 AM
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Replies: 5
Views: 1,385
Those questions are like going into a car...
Those questions are like going into a car dealership, buying a car, and saying "How do I drive?". They hint at no prior knowledge to build on. Answering them as asked will get you nowhere, and is...
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Forum: Bioinformatics
04-03-2013, 04:20 PM
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Replies: 14
Views: 9,937
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Forum: Bioinformatics
03-29-2013, 12:16 PM
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Replies: 4
Views: 2,465
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