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Search: Posts Made By: mrfox
Forum: Bioinformatics 02-14-2017, 05:22 AM
Replies: 4
Views: 1,172
Posted By mrfox
Thank you both. Yes it depends on the ORF and...

Thank you both. Yes it depends on the ORF and orientation. Technically, we have to concatenate the exon DNA sequences of a transcript and count the position of the mutation and translate the short...
Forum: Bioinformatics 02-13-2017, 08:16 AM
Replies: 4
Views: 1,172
Posted By mrfox
quickly extract amino acid sequence

Hi all,

I wonder if there is a handy tool or database to extract the amino acid sequence of a given coordinate on the human DNA. For example, given chr2:25457242, how to know what is the amino...
Forum: Bioinformatics 11-21-2016, 11:01 AM
Replies: 1
Views: 1,513
Posted By mrfox
clinical RNA-Seq: batch effect

Hi all,
I have RNA-Seq data set coming from a clinical trial. The samples were extracted and sequenced at different days. That is, each individual sample could be processed separately. When a sample...
Forum: Bioinformatics 02-17-2016, 07:21 PM
Replies: 1
Views: 922
Posted By mrfox
Tumor fraction and CNV: a loop?

I am trying to detect somatic CNV using matched tumor/normal exome sequencing data.

I found that popular tools such as EXCAVATOR, ExomeCNV etc require tumor fraction or cellularity as an input...
Forum: Bioinformatics 01-26-2016, 10:24 AM
Replies: 0
Views: 1,458
Posted By mrfox
Marker file of exome sequencing data for GISTIC

Hi all,
Does any one have an idea how to create the "marker file" for GISTIC2? Assume that the data are whole exome sequencing for matching Normal/Tumor pairs and Circular Binary Segmentation(CBS)...
Forum: Bioinformatics 01-26-2016, 09:48 AM
Replies: 0
Views: 1,264
Posted By mrfox
"markers" in CBS of DNACopy

Hi all,

In the output of Circular Binary Segmentation(CBS) of DNACopy, there is a column "num.mark". I am not clear what a "marker" represents.
Any input will be appreciated!
Forum: Bioinformatics 01-20-2016, 08:26 AM
Replies: 0
Views: 1,125
Posted By mrfox
Somatic CNV tools for WES

Hi all,

I did not follow the recent advances about tools for CNA detection using whole exome sequencing data of Tumor-Normal pairs.

Do you have any recommendations(in my mind, ExomeDepth,...
Forum: Bioinformatics 01-07-2016, 06:39 AM
Replies: 0
Views: 1,175
Posted By mrfox
CNV cutoff to define homozygous deletion

Hi all,

Assuming I have Exome sequencing of a tumor/normal pair and the somatic CNA has been detected and CBS has been performed.

Do you have any recommendation of the cutoff of the log2 ratio...
Forum: Bioinformatics 12-15-2015, 08:13 AM
Replies: 0
Views: 1,420
Posted By mrfox
Convert Broad Firehose RSEM to TPM

Hi all,

Does any one have an idea of reliably convert the RSEM expression values from the Broad Institute Firehose TCGA data to TPM?

Or, is there a place to download the TPM value directly?
...
Forum: Bioinformatics 11-05-2015, 07:30 PM
Replies: 1
Views: 962
Posted By mrfox
tools/approaches to detect mutated pathways

hi all,

I have exome sequencing data of 50 patients. And my collaborator is specifically interested in a pathway including about 30 genes. I wonder if there is recommendation about the tool to...
Forum: Bioinformatics 10-28-2015, 07:21 AM
Replies: 0
Views: 1,195
Posted By mrfox
Nanostring data: pathway analysis

Hi all,

Nanostring data usually have a panel of about 800 genes. I wonder what tools or approaches do you use for pathway analysis, given the DE list (say, 100 DE genes).

Thanks!
Forum: Bioinformatics 10-26-2015, 02:27 PM
Replies: 0
Views: 819
Posted By mrfox
Unhappy help: mutations affecting pathway

Hi all,

I have the somatic mutations of 2 group of patients: responder and non-responder. I would like to show that the non-responder group is due to the damage of a specific pathway (e.g. WNT). ...
Forum: Bioinformatics 09-09-2015, 06:43 PM
Replies: 4
Views: 1,878
Posted By mrfox
Hi lpachter, Thanks a lot for the advice. I...

Hi lpachter,

Thanks a lot for the advice. I agree that lacking biological replicates would not lead to meaningful p-values. I just checked the relative expression ratios, according to my...
Forum: Bioinformatics 07-20-2015, 05:40 AM
Replies: 4
Views: 1,878
Posted By mrfox
Thanks dpryan for the reply. I agree with you...

Thanks dpryan for the reply. I agree with you that the gene/transcript length, GC content, 3'UTR bias should be considered. I will definitely try Salmon when having a chance.
Forum: Bioinformatics 07-17-2015, 11:22 AM
Replies: 4
Views: 1,878
Posted By mrfox
RSEM: directly compare the gene expression ratio in the same sample?

Hi all,
I wonder if I could use RSEM value to compare the expression level of 2 genes directly? For instance, gene A's RSEM value is 100, gene B's RSEM value is 200. Then can I say the expression...
Forum: Bioinformatics 04-14-2015, 11:37 AM
Replies: 0
Views: 880
Posted By mrfox
NA gene expression values in TCGA RNA_Seq Level3 data

hi all,

I found a lot of "NA" values in the TCGA normalized RSEM gene expression data. Could anyone give me a hint what they are and where they came from?

Thanks a lot!
Forum: Bioinformatics 03-09-2015, 07:54 AM
Replies: 1
Views: 1,417
Posted By mrfox
Tumor Purity for Exome Sequencing Data

hi all,

I am wondering if anybody has recommendation for software tools that work well for inferring tumor purity for exome sequencing data.

Thanks a lot!
Forum: Bioinformatics 01-27-2015, 05:25 AM
Replies: 3
Views: 1,916
Posted By mrfox
I gave up finally and I used VarScan2. Sorry I am...

I gave up finally and I used VarScan2. Sorry I am not able to help on ExomeCNV.
Forum: Bioinformatics 11-01-2014, 01:12 PM
Replies: 1
Views: 1,725
Posted By mrfox
Germine copy number variation detection?

Hi all,
I have the normal tissue of about 20 cancer patients with family cancer history. We would like to perform exome sequencing to identify germline mutations, especially germline copy number...
Forum: Core Facilities 06-15-2014, 07:07 PM
Replies: 2
Views: 9,704
Posted By mrfox
Exclamation !!Urgent help: identifying CNV of an interesting region by targeted sequencing

Hi all,
My collaborator is interested in a region (about 8M bp long), that has been reported to susceptible to amplification/deletions.

Our goal is to perform sequencing experiments to...
Forum: Bioinformatics 03-19-2014, 05:44 PM
Replies: 2
Views: 1,045
Posted By mrfox
Thank you TiborNagy. I agree with you....

Thank you TiborNagy.

I agree with you. Unfortunately, I mapped the merged fastq files and the original small fastq files were deleted accidentally. I realized that properly adding readgroup...
Forum: Bioinformatics 03-18-2014, 09:14 PM
Replies: 2
Views: 1,045
Posted By mrfox
Unhappy readgroup questions

hi all,
I know that there have been many posts about readgroup in SAM/BAM format. But I am still confused.

Assume I have a sample named "Treated"sequenced with Illumina HiSeq platform. There are...
Forum: Bioinformatics 01-14-2014, 06:32 AM
Replies: 1
Views: 1,074
Posted By mrfox
validation: Exome Sequencing data

HI all,
I have 10 pairs of normal-tumor whole exome data. The mutation calling has been performed and many interesting SNVs were detected. Allele Frequency cutoff 0.05 was used.

However, our...
Forum: Bioinformatics 05-29-2013, 05:47 AM
Replies: 0
Views: 826
Posted By mrfox
Talking Re-repost: tophatfusion

hi guys,

I created a thread quite a while ago to discuss the empty result of tophatfusion at http://seqanswers.com/forums/showthread.php?t=17091&highlight=tophat+fusion.

Recently I upgraded the...
Forum: Bioinformatics 03-19-2013, 06:42 AM
Replies: 1
Views: 1,134
Posted By mrfox
H3k36me3 data: how to handle replicates?

hi all,
I wonder if there is a decent way to handle replicates when studying H3K36Me3 chip seq data. Usually the peaks for this kind of histone modification is broad.

Assume I have 3 normal...
Showing results 1 to 25 of 103

 


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