Forum: Bioinformatics
03-22-2017, 07:42 AM
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Replies: 0
Views: 1,368
Visualize just non-synonymous variants in IGV
Hello,
I used snpeff to annotate a set of variants and I would like to only visualize where a particular type of variant (non-synonymous mutations) localize on the chromosomes in the IGV.
Is...
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Forum: RNA Sequencing
02-23-2017, 07:52 AM
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Replies: 3
Views: 2,687
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Forum: Bioinformatics
09-08-2016, 10:52 AM
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Replies: 0
Views: 1,288
CummeRbund PCAplot RNA-sequencing
Hello all,
I'm using the PCAplot function in cummerbund and I was wondering if anyone knows how to display the variance explained for each principal component. The current code does not calculate...
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Forum: Bioinformatics
03-17-2016, 09:22 AM
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Replies: 2
Views: 1,079
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Forum: Bioinformatics
03-17-2016, 08:59 AM
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Replies: 2
Views: 1,079
Alignment to multiple reference sequences
Hello,
I'm interested in determining if plasmid sequences are in a NGS data set and I was thinking about creating a master fasta file with the sequences for each plasmid and then aligning NGS data...
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Forum: Bioinformatics
02-24-2016, 12:18 PM
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Replies: 0
Views: 2,969
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Forum: Bioinformatics
01-27-2016, 09:17 AM
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Replies: 5
Views: 1,786
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Forum: Bioinformatics
01-27-2016, 08:47 AM
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Replies: 5
Views: 1,786
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Forum: Bioinformatics
01-27-2016, 08:25 AM
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Replies: 5
Views: 1,786
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Forum: Bioinformatics
11-24-2015, 07:55 AM
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Replies: 0
Views: 1,713
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Forum: Bioinformatics
04-09-2015, 07:50 AM
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Replies: 0
Views: 2,210
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Forum: Bioinformatics
03-31-2015, 10:29 AM
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Replies: 3
Views: 2,975
Cuffmerge error
Hello, I am getting the following error message when using Cuffmerge:
cas-mw134-9sb9s:cufflinks-2.2.1.OSX_x86_64 bioadmin$ ./cuffmerge —p 30 -g genes_sort.gtf -s reference.txt assembly.txt
[Tue...
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Forum: Bioinformatics
03-25-2015, 06:45 AM
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Replies: 3
Views: 2,374
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Forum: Bioinformatics
03-25-2015, 06:25 AM
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Replies: 3
Views: 2,374
Can I use preproccesed bam files for Cufflinks?
This question has been asked here previously: http://seqanswers.com/forums/showthread.php?t=42408&highlight=cufflinks+preprocessed
Similarly, I have trimmed, aligned and sorted using STAR, add...
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Forum: RNA Sequencing
03-04-2015, 04:59 AM
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Replies: 3
Views: 3,514
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Forum: RNA Sequencing
03-03-2015, 08:31 AM
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Replies: 3
Views: 3,514
2nd Pass Alignment with STAR for RNA-sequencing
Hello everyone,
Firstly, thanks for reading this post. I'm performing 2nd pass alignment with STAR and I was wondering how to merge SJ.out.tab files. I'll be performing the first phase alignment...
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Forum: Bioinformatics
02-19-2015, 12:01 PM
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Replies: 5
Views: 3,677
kmcarr,
What are the differences between...
kmcarr,
What are the differences between TruSeq3-PE.fa and TruSeq3-PE-2.fa? I've downloaded the latest release of Trimmomatic and have access to the PE-2 fasta file.
Thanks.
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Forum: Bioinformatics
02-19-2015, 11:59 AM
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Replies: 5
Views: 3,677
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Forum: Bioinformatics
02-18-2015, 07:51 AM
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Replies: 5
Views: 3,677
Trimmomatic and Multiplexed Samples
Hello and thanks for reading,
I'm performing adapter trimming for the first time using Trimmomatic on paired-end reads. We solicited a third party to generate our RNA-seq libraries and they used...
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Forum: RNA Sequencing
02-26-2014, 01:56 PM
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Replies: 4
Views: 2,482
Thanks sindrle,
I've successfully imported by...
Thanks sindrle,
I've successfully imported by data into R and labeled the points on the scatterplot with gene IDs, but I am encountering another issue. I would like to modify the axis intervals in...
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Forum: RNA Sequencing
02-17-2014, 03:19 PM
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Replies: 4
Views: 2,482
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