Forum: Illumina/Solexa
01-29-2014, 05:24 PM
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Replies: 9
Views: 4,052
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Forum: Illumina/Solexa
01-29-2014, 06:38 AM
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Replies: 9
Views: 4,052
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Forum: Illumina/Solexa
01-29-2014, 05:39 AM
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Replies: 9
Views: 4,052
MiSeq 600bp sequencing problem
Hi, our Genomics Center sent me a link to the MiSeq run they are doing for us with the new 600 bp chemistry - and I notice something on the run stats that scares me:
1. Yield perfect read 1:...
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Forum: Bioinformatics
05-02-2013, 08:35 AM
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Replies: 514
Views: 225,065
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Forum: Bioinformatics
05-01-2013, 12:29 PM
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Replies: 514
Views: 225,065
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Forum: Bioinformatics
10-12-2012, 08:35 AM
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Replies: 3
Views: 1,741
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Forum: Bioinformatics
10-12-2012, 07:12 AM
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Replies: 3
Views: 1,741
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Forum: Bioinformatics
10-10-2012, 02:17 PM
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Replies: 6
Views: 4,354
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Forum: Bioinformatics
10-05-2012, 07:09 AM
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Replies: 6
Views: 4,354
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Forum: Bioinformatics
10-05-2012, 06:26 AM
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Replies: 6
Views: 4,354
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Forum: Bioinformatics
09-28-2012, 02:08 PM
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Replies: 1
Views: 982
How to find primers using biopieces?
Hi, I'm not much of a bioinformatician, and I am trying to learn how to use biopieces, which our real bioinformatician left behind on our server. Mostly it seems straightforward, but I am stumped by...
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Forum: Bioinformatics
06-01-2012, 06:41 AM
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Replies: 1
Views: 1,147
Bowtie paired read input format
Hi there, I have some fastq data that is formatted for use with Trinity, which supports unpaired reads in paired end data (that is, some sequences that are in read1.fastq are not in read2.fastq, and...
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Forum: Bioinformatics
06-01-2012, 05:53 AM
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Replies: 514
Views: 225,065
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Forum: Bioinformatics
05-09-2012, 02:40 AM
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Replies: 1
Views: 1,349
Comparing sets of contigs
Hi, I have no reference genome for my organism, and I have de novo transcriptome contigs (made from 454 and Illumina data assembled with Newbler and Trinity, respectively, then combined with Cap3)...
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Forum: Bioinformatics
04-20-2012, 04:35 AM
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Replies: 4
Views: 2,700
CAP3 to merge two assemblies?
Hi there, I have two assemblies (one from Illumina data made using Trinity, one from 454 data made using Newbler) and I would like to combine them into one assembly. It was suggested that I try CAP3...
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Forum: Bioinformatics
03-12-2012, 08:49 AM
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Replies: 5
Views: 8,335
One more question: does it matter if some reads...
One more question: does it matter if some reads are unpaired (that is, I have removed poor quality or too-short sequences, so not all reads are paired)? I think if this is a problem I need to specify...
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Forum: Bioinformatics
03-12-2012, 08:14 AM
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Replies: 5
Views: 8,335
Hi fkrueger,
Can you give me an example of...
Hi fkrueger,
Can you give me an example of the command line you would use if you had unpaired reads (like I do) in fastq format? There are a few examples in the manual, but I'm still not certain...
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Forum: Bioinformatics
03-12-2012, 07:22 AM
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Replies: 5
Views: 8,335
Use of Bowtie to remove PhiX from Illumina data
I have Illumina data that was spiked with PhiX sequences as an internal control, and I'd like to make sure those sequences are removed from my data before I try assembling it. I thought of using...
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Forum: Bioinformatics
03-06-2012, 05:25 AM
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Replies: 6
Views: 3,460
No idea, you might want to ask the original...
No idea, you might want to ask the original script writer, who is cited in the comments at the top of the script (and there is also a reference to another SeqAnswers thread there that might answer...
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Forum: Bioinformatics
03-06-2012, 12:21 AM
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Replies: 6
Views: 3,460
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Forum: Bioinformatics
02-23-2012, 03:09 AM
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Replies: 12
Views: 3,795
Hi- so far I've been testing Trinity for my...
Hi- so far I've been testing Trinity for my assemblies, though I was also thinking of using the Rnnotator pipeline (JGI Galaxy server), which uses Velvet. I'm not sure I understand what you mean by...
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Forum: Bioinformatics
02-22-2012, 04:25 AM
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Replies: 12
Views: 3,795
Deepak, I suggest you post your question in a...
Deepak, I suggest you post your question in a thread that is relevant- if you have a reference genome you are not doing de novo transcriptome assembly, and you are also not looking at differential...
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Forum: Bioinformatics
02-21-2012, 07:16 AM
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Replies: 12
Views: 3,795
I am also going to be mapping short reads to...
I am also going to be mapping short reads to assembled contigs from multiple samples- and my strategy is to assemble the contigs together in Trinity, then map the reads to the contigs. I would assume...
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Forum: De novo discovery
02-10-2012, 08:58 AM
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Replies: 7
Views: 5,155
De novo transcriptome quality metrics?
Hi everyone
I'm going to be making several de novo transcriptome assemblies (using different software), and I wish to compare them. What metrics are best for this? I don't have a reference genome....
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Forum: Bioinformatics
01-27-2012, 10:02 AM
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Replies: 6
Views: 24,829
I've tried the 13-mer adapter end sequence with...
I've tried the 13-mer adapter end sequence with the FastXtoolkit (Clip), and it didn't remove any reads. However, when I use the full primer sequences, reads are clipped and removed. I'm going to try...
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