Forum: Bioinformatics
02-14-2017, 06:22 AM
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Replies: 4
Views: 1,252
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...
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Forum: Bioinformatics
02-13-2017, 09:16 AM
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Replies: 4
Views: 1,252
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...
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Forum: Bioinformatics
11-21-2016, 12:01 PM
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Replies: 1
Views: 1,564
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...
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Forum: Bioinformatics
02-17-2016, 08:21 PM
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Replies: 1
Views: 1,048
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...
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Forum: Bioinformatics
01-26-2016, 11:24 AM
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Replies: 0
Views: 1,549
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)...
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Forum: Bioinformatics
01-26-2016, 10:48 AM
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Replies: 0
Views: 1,386
"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!
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Forum: Bioinformatics
01-20-2016, 09:26 AM
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Replies: 0
Views: 1,176
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,...
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Forum: Bioinformatics
01-07-2016, 07:39 AM
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Replies: 0
Views: 1,223
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...
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Forum: Bioinformatics
12-15-2015, 09:13 AM
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Replies: 0
Views: 1,544
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?
...
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Forum: Bioinformatics
11-05-2015, 08:30 PM
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Replies: 1
Views: 1,001
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...
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Forum: Bioinformatics
10-28-2015, 08:21 AM
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Replies: 0
Views: 1,281
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!
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Forum: Bioinformatics
10-26-2015, 03:27 PM
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Replies: 0
Views: 875
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). ...
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Forum: Bioinformatics
09-09-2015, 07:43 PM
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Replies: 4
Views: 2,019
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...
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Forum: Bioinformatics
07-20-2015, 06:40 AM
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Replies: 4
Views: 2,019
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Forum: Bioinformatics
07-17-2015, 12:22 PM
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Replies: 4
Views: 2,019
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Forum: Bioinformatics
04-14-2015, 12:37 PM
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Replies: 0
Views: 919
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Forum: Bioinformatics
03-09-2015, 08:54 AM
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Replies: 1
Views: 1,500
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!
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Forum: Bioinformatics
01-27-2015, 06:25 AM
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Replies: 3
Views: 2,027
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Forum: Bioinformatics
11-01-2014, 02:12 PM
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Replies: 1
Views: 1,784
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...
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Forum: Core Facilities
06-15-2014, 08:07 PM
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Replies: 2
Views: 9,828
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Forum: Bioinformatics
03-19-2014, 06:44 PM
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Replies: 2
Views: 1,090
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...
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Forum: Bioinformatics
03-18-2014, 10:14 PM
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Replies: 2
Views: 1,090
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...
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Forum: Bioinformatics
01-14-2014, 07:32 AM
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Replies: 1
Views: 1,133
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...
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Forum: Bioinformatics
05-29-2013, 06:47 AM
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Replies: 0
Views: 857
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...
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Forum: Bioinformatics
03-19-2013, 07:42 AM
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Replies: 1
Views: 1,187
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...
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