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Forum: Bioinformatics 04-09-2018, 05:32 AM
Replies: 1
Views: 391
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: 315
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: 644
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: 339
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: 594
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: 594
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: 1,713
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: 778
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: 912
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: 511
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: 808
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: 808
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: 1,041
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: 972
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: 1,134
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: 585
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: 1,766
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: 1,072
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....
Forum: Sample Prep / Library Generation 09-03-2015, 08:27 AM
Replies: 7
Views: 1,493
Posted By lre1234
What about taking the DNA that you have gotten...

What about taking the DNA that you have gotten and try doing MALBAC or some other whole genome amplification (not sure how well this would work)
Forum: Bioinformatics 08-12-2015, 09:16 AM
Replies: 0
Views: 586
Posted By lre1234
is bedtools paired-end aware?

Hi all,
This is probably a rather basic question but here it goes. Up until recently I have been doing RNA-seq using single-ended sequence reads. When using bedtools intersect, each read will...
Forum: Bioinformatics 08-02-2015, 01:05 PM
Replies: 1
Views: 388
Posted By lre1234
Help resolve a lab debate...

Hi all,
We are having a lab debate regarding short RNA sequence. Specifically, we generally we do unique mapping of the reads to the genome. After intersecting the mapped reads to the miRNAs and...
Forum: Bioinformatics 07-22-2015, 04:22 AM
Replies: 0
Views: 302
Posted By lre1234
How to create a specific image

Does anyone know what application was used to make the attached image. It is common in many papers, and I would like to make a similar one. I'm just not sure what was used to create it.
Thanks
Forum: Bioinformatics 05-08-2015, 08:46 AM
Replies: 4
Views: 687
Posted By lre1234
we are using 2x150 PE reads and a 300bp insert...

we are using 2x150 PE reads and a 300bp insert size (I think, but need to double check). I guess, my question would be why throwout the reads? What would (in your opinion) be the issue with doing the...
Forum: Bioinformatics 05-08-2015, 07:04 AM
Replies: 4
Views: 687
Posted By lre1234
nonunique read mapping and snp calling

Hi all,
We are having a little debate here that we would like some other insights into.

The problem is that we are doing targeted sequencing of a few hundred genes, and plan on looking for snps...
Forum: Bioinformatics 04-22-2015, 08:59 AM
Replies: 0
Views: 608
Posted By lre1234
Mate-pair sequence structural variants

I was given a mate-pair whole genome dataset that was sequenced on a SOLID 5500xl. I was interested in knowing if anyone has had any experience in doing structural variant calling (CNV, LOH,...
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