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Forum: Bioinformatics 04-16-2019, 04:15 PM
Replies: 0
Views: 636
Posted By cmccabe
filter secondary reads in bam with pysam

I am new to python and trying to learn. The below is an attempt to filter out secondary reads in a all bam files in a directory using pysam. I ran mark duplicates and got an error on several bam...
Forum: Illumina/Solexa 04-16-2019, 04:52 AM
Replies: 1
Views: 524
Posted By cmccabe
Nextseq500 output from bcl2fastq 2.20

After bcl2fastq the below is what my first two lines of R1 and R2 look like. Being new to Illumina data I don't think it looks right and wanted to confirm. Thank you :).

R1
...
Forum: Illumina/Solexa 09-21-2018, 07:11 AM
Replies: 2
Views: 1,572
Posted By cmccabe
microserver direct connect to nextseq 500

Is it possible to tether/direct connect via cat 6 to the nextseq500? The idea would be to run bcl2fastq on the server. The sequencing data would transfer to the run folder onboard the instrument then...
Forum: Bioinformatics 07-16-2018, 11:47 AM
Replies: 1
Views: 695
Posted By cmccabe
Ilummina data transfer from sequencer

Is there an api or alternative that can be used to transfer the fastq from the nextseq 550 to a centos server? I am familiar with ion torrent data where this is possible but am not sure how or if it...
Forum: General 04-04-2017, 11:39 AM
Replies: 1
Views: 953
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, 03:49 AM
Replies: 1
Views: 1,580
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, 04:10 AM
Replies: 0
Views: 1,358
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, 03:38 AM
Replies: 1
Views: 1,536
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, 03:33 PM
Replies: 1
Views: 2,081
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, 03:35 PM
Replies: 6
Views: 2,172
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, 10:15 AM
Replies: 6
Views: 1,125
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, 10:07 AM
Replies: 6
Views: 1,125
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, 09:49 AM
Replies: 6
Views: 1,125
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, 09:42 AM
Replies: 6
Views: 1,125
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, 07:40 AM
Replies: 3
Views: 2,930
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, 04:12 AM
Replies: 3
Views: 2,930
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, 02:42 PM
Replies: 0
Views: 665
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, 11:28 AM
Replies: 0
Views: 782
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, 09:57 AM
Replies: 0
Views: 1,041
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, 02:16 PM
Replies: 0
Views: 1,068
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, 04:53 AM
Replies: 14
Views: 2,588
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, 08:16 AM
Replies: 4
Views: 1,782
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, 07:34 AM
Replies: 4
Views: 1,782
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.


cmccabe@DTV-A5211QLM:~/Desktop/NGS$ cat /home/cmccabe/Desktop/vcf/getrm_NA12878_IDT_targets.vcf |...
Forum: Bioinformatics 12-05-2015, 08:31 AM
Replies: 4
Views: 1,782
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, 04:04 AM
Replies: 16
Views: 1,809
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 :).
Showing results 1 to 25 of 353

 


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