Forum: Bioinformatics
06-05-2018, 07:57 PM
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Replies: 0
Views: 800
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Forum: Bioinformatics
10-27-2015, 05:42 AM
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Replies: 3
Views: 1,915
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Forum: Bioinformatics
09-24-2015, 07:20 PM
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Replies: 4
Views: 1,522
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Forum: Bioinformatics
09-24-2015, 05:52 AM
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Replies: 4
Views: 1,522
thank you for your replying, dpryan:
because...
thank you for your replying, dpryan:
because the mRNA seq of these two isoforms are nearly the same. Most of the reads mapped to NM_001130147.1 can also be mapped to NM_001130148.1. So I think the...
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Forum: Bioinformatics
09-24-2015, 03:46 AM
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Replies: 4
Views: 1,522
strange output from RSEM
hi,
I use RSEM (http://deweylab.biostat.wisc.edu/rsem/README.html) to analysis my RNA-seq data and want to summarize expression level of each RefSeq ID.
the command I used is as below:...
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Forum: Bioinformatics
06-11-2014, 04:32 AM
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Replies: 0
Views: 1,578
TCGA gene expression vs CNV
Hi,
I want to explore the correlation between specific gene expression level with its CNV status among TCGA GBM data.
Scatterplot is enough for me. in my scatterplot x is gene expression value and...
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Forum: Bioinformatics
05-03-2014, 09:49 AM
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Replies: 3
Views: 5,976
Hi blancha
thank you for your replying. your...
Hi blancha
thank you for your replying. your replying helps me a lot.
just three further questions
1. I check mean and sd of my data before and after reciprocal transformation. I found that the sd...
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Forum: Bioinformatics
05-03-2014, 06:58 AM
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Replies: 3
Views: 5,976
simple question about Z score and P value in R
Hi
I have a list and I calculate Z score and P value in R as below
Z.score=(0.52-mean(data))/sd(data)
P.value=2*pnorm(-abs(Z.score))
and P.value is 0.028 (0.52 is in my list "data")
but I...
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Forum: Bioinformatics
04-20-2014, 03:32 AM
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Replies: 0
Views: 923
How to show two datasets on one tracks
Hi,
I have two pol2 chip-seq datas come from the same cell line with two conditions. I want to show same specific genes to display different pol2 binding profiles.
I want to show them on the same...
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Forum: Bioinformatics
12-05-2013, 06:17 AM
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Replies: 0
Views: 895
tools to identify chromatin domain
HI,
I want to find domains on chromatin using my histone chip-seq data.
do you recommand some useful tools such as tool from JL Larson (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992069/). this...
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Forum: Bioinformatics
09-19-2013, 10:20 PM
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Replies: 9
Views: 6,689
HI everyone,
I`m back. I think there are two...
HI everyone,
I`m back. I think there are two ways which may work
1. align RNA-seq reads to mRNA seq (eg. refseq) then merge all the isoform to calculate gene expression and compare gene expression...
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Forum: Bioinformatics
08-25-2013, 08:54 PM
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Replies: 1
Views: 1,469
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Forum: Bioinformatics
08-10-2013, 01:17 AM
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Replies: 9
Views: 6,689
Thank you for your replying, kopi-o
the...
Thank you for your replying, kopi-o
the spearman correlation is almost equally as pearson, about 0.57.
I use cor.test() in R to calculate spearman and pearson correlation.
I also consider my...
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Forum: Bioinformatics
08-09-2013, 04:53 AM
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Replies: 9
Views: 6,689
How to compare RNA-seq with microarray
HI,
I want to compare my RNA-seq with microarray which is found on GEO to indicate the highly correlation between them. I search many papers but found little information about details of comparing...
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Forum: Bioinformatics
07-27-2013, 10:39 PM
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Replies: 1
Views: 982
question about affy microarray annotation on UCSC
HI,
To my knockledge, microarry use short probe to detect mRNA level, So the sequence of probe should be very short. However the annotation of U133 plus2 or others on UCSC genome browser can be very...
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Forum: Bioinformatics
02-12-2013, 07:50 AM
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Replies: 2
Views: 1,166
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Forum: Bioinformatics
02-11-2013, 08:32 AM
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Replies: 2
Views: 1,166
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Forum: Bioinformatics
06-07-2012, 07:10 PM
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Replies: 2
Views: 1,307
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Forum: Bioinformatics
06-07-2012, 06:40 AM
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Replies: 2
Views: 1,307
little mutations were found by samtools mpileup
HI:
I used samtools mpileup to to find mutations. My sample genome is relative small and the coverage is about 1000X (illumina paired-end 90bp)
I used following code to generate VCF:
samtools...
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Forum: Genomic Resequencing
05-03-2012, 07:28 PM
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Replies: 0
Views: 1,495
question about CREST PCR template file
HI:
I used CREST to find somatic mutation, according to CREST paper (http://www.nature.com/nmeth/journal/v8/n8/full/nmeth.1628.html) one of output files is DNA template file for PCR validation, but...
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Forum: Bioinformatics
04-26-2012, 07:39 PM
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Replies: 0
Views: 1,656
CREST remove duplicate reads
HI:
I use CREST (http://www.stjuderesearch.org/site/lab/zhang) to find SV in cancer genome by whole genome sequencing (illumina paired-end 90bp, the length of fragment is ~600bp).
In CREST.pl a...
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Forum: Bioinformatics
02-26-2012, 06:00 PM
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Replies: 3
Views: 2,685
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Forum: Bioinformatics
02-26-2012, 05:22 AM
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Replies: 0
Views: 999
aviable tools for gene collapsing
Hi:
I am working on gene annotations from different groups such as Refseq, UCSC, vega and I want to collapse genes or transcripts generated by Alternative splicing or Alernative start site to unify...
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Forum: Bioinformatics
01-10-2012, 04:00 AM
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Replies: 0
Views: 2,406
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Forum: Bioinformatics
01-05-2012, 06:31 PM
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Replies: 7
Views: 3,928
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