Forum: General
11-07-2019, 12:01 PM
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Replies: 0
Views: 2,371
genomic reference file question
Would anyone happen to know of a source where I could download the genomic coordinates of exon-intron splice sites. Basically all the the splice donor and acceptor sites. I know I could generate...
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Forum: Bioinformatics
03-08-2019, 09:40 AM
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Replies: 7
Views: 1,269
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Forum: Bioinformatics
03-08-2019, 08:03 AM
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Replies: 7
Views: 1,269
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Forum: Bioinformatics
03-08-2019, 05:59 AM
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Replies: 7
Views: 1,269
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Forum: Bioinformatics
03-06-2019, 10:52 AM
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Replies: 7
Views: 1,269
SNP Allele frequency data
Hi All,
I have a list of a few thousands SNP that I am trying to get the population allele frequency data for. Ideally, I would like the frequencies for all 26 of the populations within the 1000...
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Forum: Bioinformatics
11-26-2018, 07:04 AM
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Replies: 2
Views: 1,298
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Forum: Bioinformatics
10-15-2018, 07:42 AM
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Replies: 1
Views: 994
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Forum: Bioinformatics
04-09-2018, 06:32 AM
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Replies: 1
Views: 1,232
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Forum: Bioinformatics
03-29-2018, 08:43 AM
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Replies: 0
Views: 646
Somatic mutation calling with out normal samples
Hi all,
I have a question, a collaborator of mine has a set of primary and metastatic tumor samples that they are interesting in doing exome or genome sequencing (not sure which one yet). The issue...
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Forum: Bioinformatics
08-12-2017, 05:56 PM
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Replies: 1
Views: 1,214
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Forum: Bioinformatics
05-12-2017, 09:40 AM
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Replies: 0
Views: 762
LOH method
Hi all,
I have some exome-seq data on families with a rare disease and are consanguineous. Our thought is that there would be some regions of LOH. I have never done LOH mapping, but was wondering...
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Forum: Bioinformatics
02-15-2017, 05:49 AM
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Replies: 2
Views: 1,106
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Forum: Bioinformatics
02-13-2017, 01:04 PM
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Replies: 2
Views: 1,106
How many unannotated SNPs?
Hi All,
I have a quick question. I'm doing some exome sequencing, and after all of the mapping, and annotating steps, I'm starting to go through the downstream analysis. One thing that I am looking...
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Forum: Bioinformatics
01-25-2017, 05:07 AM
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Replies: 3
Views: 3,937
Hi,
I do a lot of short RNA-seq and here are...
Hi,
I do a lot of short RNA-seq and here are some thoughts (but there are other ways of doing things that work well):
1. Agreed that adapter trimming is a must or most of your reads will not map....
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Forum: Bioinformatics
01-12-2017, 12:52 PM
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Replies: 0
Views: 1,285
mutsig like program
Hi All,
I'm going to be doing some exome sequence analysis on non-cancer samples. I'm interested if anyone has an information on good program that can predict the significantly mutated genes in the...
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Forum: Bioinformatics
11-30-2016, 01:15 PM
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Replies: 1
Views: 1,507
Data Analysis question
Hi all,
I'm going through some exome-seq data (10 samples), and following a "standard" pipeline - BWA, HaplotypeCaller, GenotypeGVCF, etc.. nothing too fancy.
My question is on the VQSR step....
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Forum: Sample Prep / Library Generation
10-13-2016, 07:05 AM
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Replies: 1
Views: 1,193
RIP-seq library prep - single or paired-end reads?
Hi all,
I'm going to be helping a colleague with analyzing some RIP-seq data. We just had a question regarding the library prep protocol. Specifically, is it better to use paired-end or single-ended...
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Forum: Bioinformatics
09-21-2016, 05:26 AM
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Replies: 2
Views: 1,479
The command is:
The output looks...
The command is:
The output looks exactly like what it would be if you use 'intersect' rather than coverage. Also, the usage and options summary has different options than what is here:...
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Forum: Bioinformatics
09-20-2016, 07:46 PM
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Replies: 2
Views: 1,479
weird compiling of bedtools
Hi all,
I am updating to the newest version of bedtools (v2.26). Upon compiling the application, I get a weird effect. Essentially, when I go and use the 'coverage' command, I get an output that is...
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Forum: Bioinformatics
09-09-2016, 05:05 AM
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Replies: 8
Views: 1,952
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Forum: Bioinformatics
09-01-2016, 10:16 AM
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Replies: 1
Views: 1,922
Potentially corrupted BAM files
Hi all,
I have a question about detecting possible corruptions to BAM files. Essentially, we had a serious hard drive issue and failure across our network. While we have been able to restore our...
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Forum: Bioinformatics
03-04-2016, 10:16 AM
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Replies: 0
Views: 1,940
mutect2 in a targeted region
Hi all,
I am using Mutect2 to call variants from exome seq samples (tumor/normal pair). I amusing the -L flag to call only in the targeted exome and not the whole genome. Yet, when it runs it seems...
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Forum: Bioinformatics
12-22-2015, 08:15 AM
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Replies: 0
Views: 1,112
MuTect and RNA-seq
Hi all,
I was wondering if anyone has used MuTect to call variants from RNA-seq data? I have total RNA-seq data for tumor and matched normal samples, and am wondering if MuTect would work. As...
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Forum: General
12-17-2015, 05:58 AM
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Replies: 16
Views: 2,862
As some one who did a solely molecular biology...
As some one who did a solely molecular biology based PhD and has since transferred into the computational world, I think that this site is somewhat biased towards the bioinformatics people. (this is...
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Forum: RNA Sequencing
12-15-2015, 08:24 AM
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Replies: 1
Views: 1,944
Annotated junctions file for STAR
Hi all,
Does anyone know where I would be able to get an annotated splice junction file that I could use with STAR? I've been searching for one, but have been having trouble trying to locate one....
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