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Forum: General 04-04-2017, 12:39 PM
Replies: 1
Views: 617
Posted By cmccabe
gene inheritence other than OMIM

Is there a site or reference or database, other than OMIM, to obtain gene inheritance, such as AD or AR, etc...Thank you :).
Forum: Bioinformatics 03-01-2017, 04:49 AM
Replies: 1
Views: 620
Posted By cmccabe
add missing annotations to vcf

I am using bcftools version 1.3.1 and trying to add undefined annotations to a vcf before using bgzip and tabix.

If I try to run the norm command on the vcf I get:

bcftools norm -m-both -o...
Forum: Bioinformatics 02-01-2017, 05:10 AM
Replies: 0
Views: 523
Posted By cmccabe
annovar multi-thread option syntax error

I am trying to use the muli-threading option in annovar and not having any luck. Both of my attempts below have yielded syntax errors. I am not sure whats wrong or where to place the -thread option....
Forum: General 12-22-2016, 04:38 AM
Replies: 1
Views: 1,135
Posted By cmccabe
General IGV question about pileup

In IGV what does a variant found only in white space denote. I don't think its real but trying to figure it out. For example, in the attached all the C are located in the white space. Thank you :).
Forum: Bioinformatics 08-10-2016, 04:33 PM
Replies: 1
Views: 1,187
Posted By cmccabe
UCSC liftover or NCBI remap for hg19 to hg38 conversion

I am going to convert many hg19 coordinates into hg38 and just wanted to get opinions as to liftover or remap. Which is best/ more optimal for this type of data? Thank you :).
Forum: Bioinformatics 08-04-2016, 04:35 PM
Replies: 6
Views: 1,393
Posted By cmccabe
I have been using nexus copy number for many...

I have been using nexus copy number for many years (primarily for array cgh. It it very easy to use, flexible (both platfom independent and runs in windows, mac, and linux), and newest version of...
Forum: Bioinformatics 07-14-2016, 11:15 AM
Replies: 6
Views: 624
Posted By cmccabe
Here is the output: iostat -d Linux...

Here is the output:


iostat -d
Linux 3.19.0-64-generic (DTV-A5211QLM) 07/14/2016 _x86_64_ (16 CPU)

Device: tps kB_read/s kB_wrtn/s kB_read kB_wrtn
sda ...
Forum: Bioinformatics 07-14-2016, 11:07 AM
Replies: 6
Views: 624
Posted By cmccabe
I will definitely take a look at iostat. Thank...

I will definitely take a look at iostat. Thank you :).
Forum: Bioinformatics 07-14-2016, 10:49 AM
Replies: 6
Views: 624
Posted By cmccabe
Thanks, I am moving to a cluster server soon that...

Thanks, I am moving to a cluster server soon that has dedicated PCIe SSD to help with I/o issues. Thanks.
Forum: Bioinformatics 07-14-2016, 10:42 AM
Replies: 6
Views: 624
Posted By cmccabe
bedtools makes ubuntu 14.04 slow

When I run bedtools 2.25.0 covereBed, the command below does run.


coverageBed -d -g custom.genome.txt -a targets.bed -b file.txt > base_counts.txt



There are 11.5 millino bases in each...
Forum: Ion Torrent 07-09-2016, 08:40 AM
Replies: 3
Views: 2,124
Posted By cmccabe
I will call them on Monday, just wanted to see if...

I will call them on Monday, just wanted to see if iother users might have a similar experience or suggestions. Thanks :).
Forum: Ion Torrent 07-09-2016, 05:12 AM
Replies: 3
Views: 2,124
Posted By cmccabe
S5 reads versus proton

We recently purchased an S5 and are planning to bring a test onboard that was done on a proton. The proton using a P1 would consistently give over 90 million total reads. However, on the S5 that same...
Forum: Bioinformatics 07-08-2016, 03:42 PM
Replies: 0
Views: 440
Posted By cmccabe
add current transcript to gene

Is the best way to get the current transcript of a gene to use Biomart? That is given a list of gene ids grab the current NM_ version associated with each gene. I am using ubuntu 14.04 and was going...
Forum: Bioinformatics 02-24-2016, 12:28 PM
Replies: 0
Views: 494
Posted By cmccabe
vcftools to update vcf with gene info from bed

I am trying to add gene information to a vcf file using vcftools:


vcftools annotate \
-a genes.bed.gz \
-c CHROM,FROM,TO,GENE \
-h <(echo...
Forum: Bioinformatics 01-20-2016, 10:57 AM
Replies: 0
Views: 484
Posted By cmccabe
remove duplicates in markduplicates

If I was going to view a bam file in IGV both with duplicayes marked and then after they are removed are these commands accurate:

Flag duplicates in BAM

java -jar picard.jar MarkDuplicates \
...
Forum: Bioinformatics 12-17-2015, 03:16 PM
Replies: 0
Views: 567
Posted By cmccabe
target or bait bed file for read depth

Is it better or more accurate to generate read depth statistics using the target or bait.bed?
For example, using coverageBed I get the read depth per base in the bed. Then using awk I can detect...
Forum: Bioinformatics 12-08-2015, 05:53 AM
Replies: 14
Views: 1,785
Posted By cmccabe
I use an HP Z640 for analysis of human ngs data....

I use an HP Z640 for analysis of human ngs data. Though it was not designed optimaly, it is well suited for our current needs.
That being said a linux OS is a good choice, the flavor (ubuntu,...
Forum: Bioinformatics 12-07-2015, 09:16 AM
Replies: 4
Views: 1,239
Posted By cmccabe
Thank you very much. That seemed to solve it :)....

Thank you very much. That seemed to solve it :). This is a new way of installing that I am not used to but seems very nice. Thanks again.
Forum: Bioinformatics 12-07-2015, 08:34 AM
Replies: 4
Views: 1,239
Posted By cmccabe
Yes, you are correct I do see the files at...

Yes, you are correct I do see the files at /usr/local/bin. However, I get the below error.


[email protected]:~/Desktop/NGS$ cat /home/cmccabe/Desktop/vcf/getrm_NA12878_IDT_targets.vcf |...
Forum: Bioinformatics 12-05-2015, 09:31 AM
Replies: 4
Views: 1,239
Posted By cmccabe
vcftools-0.1.14 install no bin on ubuntu 14.04

I downloaded and unziped the master file for vcftools on github:

./autogen.sh
./configure
make
sudo make install

However, I do not have a bin folder as the install stats. I do see in the...
Forum: Bioinformatics 11-24-2015, 05:04 AM
Replies: 16
Views: 1,165
Posted By cmccabe
I am looking more into linux clusters as they...

I am looking more into linux clusters as they seem to be a better overall fit. If designed correctly they will be a good fit for the lab today and allow for growth. Thank you :).
Forum: Bioinformatics 11-17-2015, 10:28 AM
Replies: 16
Views: 1,165
Posted By cmccabe
We currently run Ion Torrent sequencing on a...

We currently run Ion Torrent sequencing on a proton. The estimate of 3.6 TB was based on that data (180 samples per year, each sample is ~20GB). Our IT department, myself included, is new to this...
Forum: Bioinformatics 11-17-2015, 09:33 AM
Replies: 16
Views: 1,165
Posted By cmccabe
The main reasons for a Virtual Machine would be...

The main reasons for a Virtual Machine would be more scalable, less upgrade cost, and I think easier for our hospital to implement and maintain. I have read different posts about hardware...
Forum: Bioinformatics 11-17-2015, 08:50 AM
Replies: 16
Views: 1,165
Posted By cmccabe
Yes you are correct, VM is Virtual Machine, thank...

Yes you are correct, VM is Virtual Machine, thank you :).
Forum: Bioinformatics 11-17-2015, 08:45 AM
Replies: 16
Views: 1,165
Posted By cmccabe
It is stated as a stand-alone server or VM but I...

It is stated as a stand-alone server or VM but I believe the VM is a better option if it is feasible. What would you recommend? Thank you :).
Showing results 1 to 25 of 349

 


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