Forum: Bioinformatics
12-17-2010, 06:20 AM
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Replies: 3
Views: 2,837
Well,
Back in the old days (like 1 year ago...
Well,
Back in the old days (like 1 year ago or so...) the basecaller produces two sets of fasta files. TCA.fa and ATG.fa if I remember correct. One file was the real file, the other one with...
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Forum: Bioinformatics
12-17-2010, 02:53 AM
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Replies: 12
Views: 10,110
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Forum: Bioinformatics
12-16-2010, 07:04 AM
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Replies: 3
Views: 2,837
454 CWF files
Hi fellow sequence analysts.
I am working on a 454 basecalling project and I have 2 main questions/problems.
1) It really would help me if someone could tell me a method to get the controlbead...
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Forum: Bioinformatics
11-30-2010, 07:04 AM
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Replies: 1
Views: 2,334
Abyss-PE error
Hi community,
I am currently involved in a rather complex project where we are hunting for causal SNPs in a species that has no assembled genome at the moment. We are planning on sequencing some...
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Forum: Bioinformatics
06-25-2010, 07:19 AM
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Replies: 16
Views: 4,448
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Forum: Bioinformatics
06-25-2010, 06:15 AM
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Replies: 16
Views: 4,448
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Forum: Bioinformatics
05-27-2010, 04:35 AM
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Replies: 5
Views: 1,907
I'm glad to see people actually using the VIP...
I'm glad to see people actually using the VIP pipeline.
We have been using the pipeline internally for almost a year now. But eventually, some bug will appear here and there. Please report any bug...
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Forum: Bioinformatics
05-27-2010, 03:28 AM
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Replies: 7
Views: 3,510
I just checked out their site and found the...
I just checked out their site and found the following thing.
SOAPindel: SOAPindel is developed to find the insertion and deletion specially for re-sequence technology : Coming soon.
I am just...
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Forum: Bioinformatics
05-27-2010, 02:56 AM
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Replies: 7
Views: 3,510
Well, I can tell you the following.
I have...
Well, I can tell you the following.
I have simulated loads of data. I have generated datasets with more than a billion reads where error profiles/PCR errors/sequencing errors were simulated and...
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Forum: Bioinformatics
05-27-2010, 02:42 AM
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Replies: 7
Views: 3,510
SOAP2 and deletions/insertions
I was told that SOAP should be able to detect deletions and insertions up to 3bp.
So i made a reference file and a file with a normal read and some reads with 1,2,3 bp deleted and inserted. Just...
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Forum: Bioinformatics
04-23-2010, 04:54 AM
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Replies: 10
Views: 9,344
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Forum: Bioinformatics
04-23-2010, 04:19 AM
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Replies: 10
Views: 9,344
we did our first RNA seq run last week and the...
we did our first RNA seq run last week and the first results came back today. I have to admint that my collegeau did all the work, I just had some discussions with him and looked at some graphs he...
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Forum: Bioinformatics
04-23-2010, 02:07 AM
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Replies: 3
Views: 2,543
Abyss @ 454
Hi there,
Is ABYSS designed for assembly of 454 reads?
# ./ABYSS -k25 -o /data/454/data/_Test_assembly /data/454/data/2.TCA.454Reads.fna
gives me the following
2.TCA.454Reads.fa' is an...
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Forum: Illumina/Solexa
04-14-2010, 08:09 AM
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Replies: 28
Views: 13,058
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Forum: Illumina/Solexa
04-14-2010, 02:56 AM
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Replies: 28
Views: 13,058
I understand that the directional RNA seq on...
I understand that the directional RNA seq on illumina is only for mRNA? Is there a total RNA protocol/kit available somewhere?
I know SOLID has a total RNA directional sequencing kit, but i don't...
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Forum: Bioinformatics
12-14-2009, 09:53 AM
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Replies: 3
Views: 2,865
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Forum: 454 Pyrosequencing
12-14-2009, 08:14 AM
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Replies: 7
Views: 3,220
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Forum: 454 Pyrosequencing
12-13-2009, 03:42 PM
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Replies: 7
Views: 3,220
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Forum: Genomic Resequencing
08-26-2009, 08:38 AM
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Replies: 9
Views: 5,164
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Forum: General
08-26-2009, 07:36 AM
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Replies: 4
Views: 19,934
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Forum: Genomic Resequencing
08-26-2009, 07:34 AM
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Replies: 9
Views: 5,164
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Forum: 454 Pyrosequencing
08-26-2009, 07:32 AM
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Replies: 15
Views: 9,414
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Forum: Bioinformatics
08-12-2009, 01:31 AM
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Replies: 33
Views: 17,644
Hi there, i am under some pressure to deliver...
Hi there, i am under some pressure to deliver results from a solexa run. They did a run, and all i had to do was give them a list of variants.
Problem is, i ran bowtie, give them the list. They...
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Forum: Bioinformatics
08-10-2009, 08:04 AM
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Replies: 18
Views: 14,834
hi there again...
The reasons I am trying...
hi there again...
The reasons I am trying BWA (still hasn't worked... ) is because I am analyzing illumina data for counting variant frequencies for a pool of several patients.
So far so good,...
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Forum: Bioinformatics
08-05-2009, 08:17 AM
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Replies: 514
Views: 224,060
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