SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 74
Search took 0.01 seconds.
Search: Posts Made By: tujchl
Forum: Bioinformatics 06-05-2018, 06:57 PM
Replies: 0
Views: 556
Posted By tujchl
Do you know why the quantification results from RSEM were deleted from TCGA?

hi, all
I just want to download the lastest RNA-seq data from TCGA (https://portal.gdc.cancer.gov/repository) and do some analyze. I found that the isoform quantification results from RSEM...
Forum: Bioinformatics 10-27-2015, 04:42 AM
Replies: 3
Views: 1,692
Posted By tujchl
you can upload your own genome sequence (usually...

you can upload your own genome sequence (usually fasta format) into IGV and visualize your outcome. you can upload your genome file via genome->upload genome from file
Forum: Bioinformatics 09-24-2015, 06:20 PM
Replies: 4
Views: 1,276
Posted By tujchl
Thank you, dpryan To be honest, I didn`t read...

Thank you, dpryan
To be honest, I didn`t read the papper. Now I think it`s the time to read it.
Forum: Bioinformatics 09-24-2015, 04:52 AM
Replies: 4
Views: 1,276
Posted By tujchl
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...
Forum: Bioinformatics 09-24-2015, 02:46 AM
Replies: 4
Views: 1,276
Posted By tujchl
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:...
Forum: Bioinformatics 06-11-2014, 03:32 AM
Replies: 0
Views: 1,375
Posted By tujchl
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...
Forum: Bioinformatics 05-03-2014, 08:49 AM
Replies: 3
Views: 5,191
Posted By tujchl
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...
Forum: Bioinformatics 05-03-2014, 05:58 AM
Replies: 3
Views: 5,191
Posted By tujchl
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...
Forum: Bioinformatics 04-20-2014, 02:32 AM
Replies: 0
Views: 781
Posted By tujchl
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...
Forum: Bioinformatics 12-05-2013, 05:17 AM
Replies: 0
Views: 763
Posted By tujchl
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...
Forum: Bioinformatics 09-19-2013, 09:20 PM
Replies: 9
Views: 6,191
Posted By tujchl
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...
Forum: Bioinformatics 08-25-2013, 07:54 PM
Replies: 1
Views: 1,258
Posted By tujchl
where I can do my analysis as before in TCGA data browser

Hi,

I was used to use data browser (http://tcga-portal.nci.nih.gov/tcga-portal/AnomalySearch.jsp) in TCGA to see differential expression in cancer (AgilentG4502A_07 log2 tumor/normal ratio) but...
Forum: Bioinformatics 08-10-2013, 12:17 AM
Replies: 9
Views: 6,191
Posted By tujchl
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...
Forum: Bioinformatics 08-09-2013, 03:53 AM
Replies: 9
Views: 6,191
Posted By tujchl
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...
Forum: Bioinformatics 07-27-2013, 09:39 PM
Replies: 1
Views: 808
Posted By tujchl
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...
Forum: Bioinformatics 02-12-2013, 06:50 AM
Replies: 2
Views: 1,023
Posted By tujchl
Thank you very much Jeremy :). It is excellent...

Thank you very much Jeremy :). It is excellent way to cluster my target genes.
Forum: Bioinformatics 02-11-2013, 07:32 AM
Replies: 2
Views: 1,023
Posted By tujchl
Can you give me some suggestions about my analysis

Hi erveyone:
I find a gene (function as transcription regulater) which is highly expressed in cancer contrast to normal. cells will go apoptosis if I knockdown this gene by shRNA.

Now I do...
Forum: Bioinformatics 06-07-2012, 06:10 PM
Replies: 2
Views: 1,089
Posted By tujchl
Thank you for your reply, I try -B, but no more...

Thank you for your reply, I try -B, but no more mutations were found.
Any one know what`s wrong?
The version of samtools is 0.1.18 (r982:295)
Forum: Bioinformatics 06-07-2012, 05:40 AM
Replies: 2
Views: 1,089
Posted By tujchl
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...
Forum: Genomic Resequencing 05-03-2012, 06:28 PM
Replies: 0
Views: 1,309
Posted By tujchl
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...
Forum: Bioinformatics 04-26-2012, 06:39 PM
Replies: 0
Views: 1,371
Posted By tujchl
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...
Forum: Bioinformatics 02-26-2012, 05:00 PM
Replies: 3
Views: 2,485
Posted By tujchl
you can try LAST (http://last.cbrc.jp/), which is...

you can try LAST (http://last.cbrc.jp/), which is very similar with blast. The speed of LAST is comparable with bowtie
Forum: Bioinformatics 02-26-2012, 04:22 AM
Replies: 0
Views: 861
Posted By tujchl
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...
Forum: Bioinformatics 01-10-2012, 03:00 AM
Replies: 0
Views: 2,213
Posted By tujchl
chip-seq normalization when two sample total reads vary largely

HI:

i am new to chip-seq and I fellow tranditional way to analyze my data.
I normalized my two chip-seq data by total reads. (I divided genome into 50bp bin), total reads here means reads after...
Forum: Bioinformatics 01-05-2012, 05:31 PM
Replies: 7
Views: 3,570
Posted By tujchl
Thank you ETHANol: I try to generate wiggle...

Thank you ETHANol:

I try to generate wiggle by SICER without filter out duplicate reads.
but difference still exists. MACS looks still smooother
Showing results 1 to 25 of 74

 


All times are GMT -8. The time now is 05:54 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO