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Search: Posts Made By: emilyjia2000
Forum: Bioinformatics 07-01-2013, 07:58 AM
Replies: 15
Views: 5,243
Posted By emilyjia2000
Thanks ernfrid for your reply! I run...

Thanks ernfrid for your reply!

I run SomaticSniper and got the results. I am not very sure the format of the output. should I define it as txt or VCF format? one column is to define somatic score,...
Forum: Bioinformatics 06-27-2013, 12:47 PM
Replies: 15
Views: 5,243
Posted By emilyjia2000
The coverage for the samples I have is around...

The coverage for the samples I have is around 50X, and I have germline and tumor pair, do you think somaticsniper also works in this case? I don't quite understand that "If your tumor purity is only...
Forum: Bioinformatics 06-26-2013, 06:29 AM
Replies: 1
Views: 825
Posted By emilyjia2000
special case on peak detections

Hello,

I have one particular case on peak detection of chip-seq data. There are three different conditions: KO, control and genomicDNA. Now I want to find the peaks only in KO that do not appear...
Forum: Bioinformatics 08-13-2012, 12:30 PM
Replies: 0
Views: 1,390
Posted By emilyjia2000
peak height on chip-seq

Hello,

I am working on peak calling of chip-seq data, I am using cisgenome to do the peak calling, after the bed files of detected peaks were loaded into IGV, it only shows the regions of the...
Forum: Bioinformatics 05-14-2012, 11:33 AM
Replies: 11
Views: 5,264
Posted By emilyjia2000
Hi Spoonman, I tried to use GATK to get the...

Hi Spoonman,

I tried to use GATK to get the coverage file, from the user guide, there is one file unclear to me, which is "-L <exome.interval_list>". how did you get exome.interval_list using...
Forum: Bioinformatics 04-18-2012, 01:09 PM
Replies: 11
Views: 5,264
Posted By emilyjia2000
Thanks spoonman for the good tips! I used...

Thanks spoonman for the good tips!

I used the author shell script to do the coverage, from the overview of coverage, the chromosome1 looks the best coverage compared to other chromosomes, I don't...
Forum: Bioinformatics 04-17-2012, 07:48 AM
Replies: 11
Views: 5,264
Posted By emilyjia2000
Thanks Spoonman! it is version issue. Now I...

Thanks Spoonman! it is version issue.

Now I sort of have another problem. I got it run through, but the results don't look right. only chromosome1 has deletion/amplifications, on other...
Forum: Bioinformatics 04-09-2012, 08:11 AM
Replies: 11
Views: 5,264
Posted By emilyjia2000
issues on running ExomeCNV

Hello,

I am trying to use ExomeCNV to do copy number analysis on exome sequencing data. I have bam files sorted already. I tried to use shell scripts for generating coverage files, one error...
Forum: Bioinformatics 04-06-2012, 12:13 PM
Replies: 9
Views: 3,946
Posted By emilyjia2000
Thanks Chand737, I tried both features: -t utr or...

Thanks Chand737, I tried both features: -t utr or -t utr5, both of them delivered the same results.

As you pointed out, I checked the category as follows:

no_feature 122533035...
Forum: Bioinformatics 04-06-2012, 11:05 AM
Replies: 9
Views: 3,946
Posted By emilyjia2000
Sorry I have two annotation files, one is the...

Sorry I have two annotation files, one is the posted, another is the one with geneid as listed in the output. two files have the same format.

Sorry I didn't make it clear.
Forum: Bioinformatics 04-06-2012, 06:47 AM
Replies: 9
Views: 3,946
Posted By emilyjia2000
Hi Chand737, The GFF used had been modified...

Hi Chand737,

The GFF used had been modified according to ensembl format as following

1 bed2gff utr5 8794025 8794051 . - . transcript_id "NM_27671"; utr5_number "0016"; gene_id "NM_27671"...
Forum: Bioinformatics 04-06-2012, 06:15 AM
Replies: 9
Views: 3,946
Posted By emilyjia2000
Hi chadn737, I used -t feature in the...

Hi chadn737,

I used -t feature in the command line and set feature to utr, please see the command i used:
htseq-count -s no -t utr -m intersection-nonempty file.sam utr.gff > urtcount.txt

the...
Forum: Bioinformatics 04-04-2012, 11:46 AM
Replies: 9
Views: 3,946
Posted By emilyjia2000
htseq-count on UTR

Hi
Does anybody know if htseq-count works on UTR? I tried it, only got gene list, there is no count in the output.
Forum: Bioinformatics 04-04-2012, 11:44 AM
Replies: 8
Views: 12,162
Posted By emilyjia2000
try picard sort, it works on me.

try picard sort, it works on me.
Forum: Bioinformatics 04-04-2012, 06:17 AM
Replies: 8
Views: 12,162
Posted By emilyjia2000
Hi Simon, Is HTseq-count possible to count...

Hi Simon,

Is HTseq-count possible to count UTR? I tried it and got nothing. If it works on UTR, any particular aspect I have to pay attention to?

THanks
Forum: Bioinformatics 03-21-2012, 01:26 PM
Replies: 34
Views: 17,826
Posted By emilyjia2000
I sort of have different question. I tried to use...

I sort of have different question. I tried to use HTseq-count to count exons, I got GFF files from NCBI mm9 and extracted the exon information to create exon.gff, but I don't know why there is 0...
Forum: RNA Sequencing 02-08-2012, 10:04 AM
Replies: 13
Views: 4,620
Posted By emilyjia2000
Thanks Jbrwn, after I erased "i ID" from the...

Thanks Jbrwn,
after I erased "i ID" from the command, same error message.
Forum: RNA Sequencing 02-08-2012, 08:21 AM
Replies: 13
Views: 4,620
Posted By emilyjia2000
Hello Simon, Thanks for the suggestion, we...

Hello Simon,

Thanks for the suggestion, we would like to see transcript level, junction reads as well, not just exon level reads. But we are sort of stuck at the exon level reads. We used tophat...
Forum: RNA Sequencing 02-07-2012, 07:05 AM
Replies: 13
Views: 4,620
Posted By emilyjia2000
Hi Simon, THanks for the reply. I searched...

Hi Simon,

THanks for the reply. I searched the tools that would help to generate exon expression level reads. for example, HTseq, Rsamtools, DEseq and DEXseq, and I am so confused and don't know...
Forum: RNA Sequencing 02-06-2012, 10:18 AM
Replies: 13
Views: 4,620
Posted By emilyjia2000
I am new to DEXseq, I just wonder if I don't have...

I am new to DEXseq, I just wonder if I don't have replicates and have only one condition, is it possible to use DEXseq to count exon level reads?
Thanks,
emily
Forum: RNA Sequencing 02-01-2012, 09:37 AM
Replies: 26
Views: 26,021
Posted By emilyjia2000
Hello, I am not sure if it is right place to...

Hello,
I am not sure if it is right place to raise my question. I would like to check on exon level reads on RNA-seq data, I don't know which tools are better on getting exon expression level. I...
Forum: Bioinformatics 01-11-2012, 01:53 PM
Replies: 8
Views: 4,896
Posted By emilyjia2000
Thanks for the suggestion, I will do it.

Thanks for the suggestion, I will do it.
Forum: Bioinformatics 01-11-2012, 09:30 AM
Replies: 8
Views: 4,896
Posted By emilyjia2000
Hi Dprayn, I don't exactly know if it...

Hi Dprayn,

I don't exactly know if it counts. When I tried to used ped file generated by vcftools from vcf file to do linkage analysis, there are a lot of Mendelian errors were generated based on...
Forum: Bioinformatics 01-10-2012, 07:41 AM
Replies: 8
Views: 4,896
Posted By emilyjia2000
Thanks dpryan, i used vcftools to generate PED...

Thanks dpryan, i used vcftools to generate PED file, which brought a trouble to me when I used it for the linkage analysis. When I checked back and found out the some of genotypes from PED doesn't...
Forum: Bioinformatics 01-10-2012, 06:58 AM
Replies: 8
Views: 4,896
Posted By emilyjia2000
Thanks for the reply. Do you know how to use...

Thanks for the reply. Do you know how to use plink to generate .ped and .map files? I presumed that this command could help to generate those.
Showing results 1 to 25 of 59

 


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