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Forum: General 11-07-2019, 11:01 AM
Replies: 0
Views: 2,120
Posted By lre1234
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...
Forum: Bioinformatics 03-08-2019, 08:40 AM
Replies: 7
Views: 1,162
Posted By lre1234
That works. Thanks. I have a couple thousand to...

That works. Thanks. I have a couple thousand to get the frequency for, so I can write some sort of wrap to let it go on and do them all.

One last question, is there a way to limit the output to...
Forum: Bioinformatics 03-08-2019, 07:03 AM
Replies: 7
Views: 1,162
Posted By lre1234
Then I must be doing something wrong (highly...

Then I must be doing something wrong (highly probable :o). I'm trying it with the wget example:


wget -q --header='Content-type:application/json' --header='Accept:application/json' \...
Forum: Bioinformatics 03-08-2019, 04:59 AM
Replies: 7
Views: 1,162
Posted By lre1234
Thanks Emily_Ensembl. This API does work, but I...

Thanks Emily_Ensembl.
This API does work, but I am still looking to get the allele frequencies for all 26 subpopulations of the 1000 Genomes. This API seems to only give the main continental...
Forum: Bioinformatics 03-06-2019, 09:52 AM
Replies: 7
Views: 1,162
Posted By lre1234
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...
Forum: Bioinformatics 11-26-2018, 06:04 AM
Replies: 2
Views: 1,078
Posted By lre1234
Separating human and mouse sequence reads from RNA-seq data

HI all,
A collaborator is doing an experiment in which their will be a human xenograph into a mouse model, followed by RNA-seq. Most likely there will be a mixture of human and mouse transcripts in...
Forum: Bioinformatics 10-15-2018, 06:42 AM
Replies: 1
Views: 840
Posted By lre1234
converting postions in a gene to genomic coordinates

Hi all,
I'm interested in a way to convert the positions in a gene to the genomic coordinates. So for example, if I have Gene X, and position 200-400 of the mRNA. I would like to be able to get...
Forum: Bioinformatics 04-09-2018, 05:32 AM
Replies: 1
Views: 1,085
Posted By lre1234
Calculating depth of coverage for overlapping paired-reads

Hi all,
I have a question on calculating the overall depth of coverage for exome or targeted panel sequencing samples.

As a simple example. If I have paired-end reads that overlap each other. A...
Forum: Bioinformatics 03-29-2018, 07:43 AM
Replies: 0
Views: 574
Posted By lre1234
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...
Forum: Bioinformatics 08-12-2017, 04:56 PM
Replies: 1
Views: 1,114
Posted By lre1234
homozygosity mapping from exome seq

Does anybody have any experience with doing homozygosity mapping with exome sequence data? Specifically, what are some good tools to use?
Forum: Bioinformatics 05-12-2017, 08:40 AM
Replies: 0
Views: 588
Posted By lre1234
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...
Forum: Bioinformatics 02-15-2017, 04:49 AM
Replies: 2
Views: 1,040
Posted By lre1234
I'm working with a standard Caucasian population...

I'm working with a standard Caucasian population group. Nothing of a isolated population which I agree would probably have a higher % of 'novel' variants.

Generally, though for anyone that has...
Forum: Bioinformatics 02-13-2017, 12:04 PM
Replies: 2
Views: 1,040
Posted By lre1234
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...
Forum: Bioinformatics 01-25-2017, 04:07 AM
Replies: 3
Views: 3,549
Posted By lre1234
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....
Forum: Bioinformatics 01-12-2017, 11:52 AM
Replies: 0
Views: 1,195
Posted By lre1234
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...
Forum: Bioinformatics 11-30-2016, 12:15 PM
Replies: 1
Views: 1,352
Posted By lre1234
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....
Forum: Sample Prep / Library Generation 10-13-2016, 06:05 AM
Replies: 1
Views: 1,075
Posted By lre1234
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...
Forum: Bioinformatics 09-21-2016, 04:26 AM
Replies: 2
Views: 1,347
Posted By lre1234
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:...
Forum: Bioinformatics 09-20-2016, 06:46 PM
Replies: 2
Views: 1,347
Posted By lre1234
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...
Forum: Bioinformatics 09-09-2016, 04:05 AM
Replies: 8
Views: 1,795
Posted By lre1234
For your miR-92a example, there are two...

For your miR-92a example, there are two homologues of this miRNA. One is on chr13 and one on chr8. The 3p arm has the same sequence for both.

>ID=MIMAT0000092;...
Forum: Bioinformatics 09-01-2016, 09:16 AM
Replies: 1
Views: 1,679
Posted By lre1234
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...
Forum: Bioinformatics 03-04-2016, 09:16 AM
Replies: 0
Views: 1,767
Posted By lre1234
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...
Forum: Bioinformatics 12-22-2015, 07:15 AM
Replies: 0
Views: 995
Posted By lre1234
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...
Forum: General 12-17-2015, 04:58 AM
Replies: 16
Views: 2,648
Posted By lre1234
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...
Forum: RNA Sequencing 12-15-2015, 07:24 AM
Replies: 1
Views: 1,790
Posted By lre1234
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....
Showing results 1 to 25 of 106

 


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