Forum: Bioinformatics
05-06-2014, 09:27 PM
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Replies: 9
Views: 6,013
dexseq results understanding
Hey, Now I am trying to find splicing differences between two tumor and two normal samples(so only one condition: N and T factors), and prepare data following your vignette, everything goes well, but...
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Forum: RNA Sequencing
12-20-2013, 01:31 AM
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Replies: 1
Views: 1,792
Possible picard bug
Hey, I am running picard to remove pcr-duplicates using MarkDuplicates.jar
on bam file porduce by tophat(with fusion-serach on), and I encount:
Exception in thread "main"...
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Forum: Bioinformatics
11-28-2013, 11:59 PM
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Replies: 1
Views: 1,904
Defuse Calculating spanning p-values Failure
Hey, could anyone help me with one problem:
when I run defuse to find gene fusions based on fastq data (illumina HISEQ, paired-end, trimed by trimglore), the software goes well until Calculating...
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Forum: Bioinformatics
07-21-2011, 04:20 AM
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Replies: 4
Views: 3,463
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Forum: Bioinformatics
07-19-2011, 01:07 AM
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Replies: 4
Views: 3,463
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Forum: Bioinformatics
07-18-2011, 06:02 AM
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Replies: 4
Views: 3,463
asking about convert ab1 file to image
I have a sequencing chromotogram file in ab1 format, I can view it in softwares like chromatogram Explorer, but I want to show the chromatogram in my manuscript, so I need convert to a image file...
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Forum: Bioinformatics
05-18-2010, 04:11 AM
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Replies: 6
Views: 3,449
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Forum: Bioinformatics
05-18-2010, 04:08 AM
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Replies: 6
Views: 3,449
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Forum: Bioinformatics
05-18-2010, 03:29 AM
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Replies: 6
Views: 3,449
yes, i should make it clear ~
the paper i consider is
"Widespread RNA editing of embedded alu elements in the human transcriptome"
in the method part, they mentioned "We obtained all human and mouse full-length cDNA sequences...
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Forum: Bioinformatics
05-18-2010, 12:00 AM
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Replies: 6
Views: 3,449
about UCSC full length cDNA
in one paper, they use downloaded full length cDNA sequences(from ucsc) to detect A-to-I rna editing by aligning to reference hg16, but when i want to repeat their work by downloading human mRNA...
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Forum: Bioinformatics
03-04-2010, 12:29 AM
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Replies: 11
Views: 3,320
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Forum: Bioinformatics
03-04-2010, 12:21 AM
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Replies: 11
Views: 3,320
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Forum: Bioinformatics
02-15-2010, 06:09 PM
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Replies: 5
Views: 2,096
the reason is 3 different David gene id (that...
the reason is 3 different David gene id (that they used when do enrichment analysis) mapped to 1 ensemble gene id, the following is the answer from the David Guys:
Ensembl gene id was integrated...
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Forum: Bioinformatics
02-09-2010, 04:58 PM
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Replies: 5
Views: 2,096
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Forum: Bioinformatics
02-08-2010, 06:15 AM
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Replies: 5
Views: 2,096
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Forum: Bioinformatics
01-21-2010, 04:43 AM
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Replies: 0
Views: 1,691
has anyone analyses GLFv3 format?
samtools can Generate genotype likelihood in the binary GLFv3 format, i want ot analyses the genotype data, but which tools can be used to analyses this GLFv3 output ?
thanks in advance
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Forum: Illumina/Solexa
01-15-2010, 05:04 PM
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Replies: 2
Views: 1,514
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Forum: Illumina/Solexa
01-14-2010, 10:02 PM
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Replies: 2
Views: 1,514
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Forum: Bioinformatics
01-09-2010, 05:03 AM
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Replies: 2
Views: 1,668
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Forum: Bioinformatics
01-07-2010, 03:50 AM
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Replies: 2
Views: 1,668
how to get snps
hello guys.
i have hundreds of locations on the human genome, and i wish to check whether they're snps and what is the minor base, is there some better way than to downlaod them all and write code...
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Forum: Bioinformatics
12-13-2009, 10:31 PM
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Replies: 2
Views: 3,453
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Forum: Bioinformatics
12-10-2009, 04:56 PM
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Replies: 8
Views: 2,661
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Forum: Bioinformatics
12-08-2009, 04:54 PM
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Replies: 8
Views: 2,661
SIFT (Sorting Intolerant From Tolerant) is a...
SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function
my work is simpler, i just want to know whether a change of bases on...
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Forum: Bioinformatics
12-07-2009, 11:37 PM
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Replies: 8
Views: 2,661
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Forum: Bioinformatics
11-25-2009, 12:08 AM
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Replies: 3
Views: 3,611
as for splicing sites, i think at least in...
as for splicing sites, i think at least in protein coding genes it should be exact the exon-intron boundary, because any error may cause frame shift.
i think you want to know the length of sequence...
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