Forum: Bioinformatics
01-11-2020, 03:52 AM
|
|
Replies: 0
Views: 1,420
optimize a execution of a pindel process
I am looking to optimize a pindel process. Below is the command used:
pindel -f refererence -i configfile -c ALL -T 16 -o sample
I then execute pindel2vcf on the output.... I was thinking...
|
|
Forum: Bioinformatics
04-16-2019, 04:15 PM
|
|
Replies: 0
Views: 2,586
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: 1,595
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: 2,961
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: 1,141
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: 1,266
|
|
Forum: Bioinformatics
03-01-2017, 03:49 AM
|
|
Replies: 1
Views: 2,932
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: 2,166
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: 2,303
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: 2,848
|
|
Forum: Bioinformatics
08-04-2016, 03:35 PM
|
|
Replies: 6
Views: 2,999
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: 1,837
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: 1,837
|
|
Forum: Bioinformatics
07-14-2016, 09:49 AM
|
|
Replies: 6
Views: 1,837
|
|
Forum: Bioinformatics
07-14-2016, 09:42 AM
|
|
Replies: 6
Views: 1,837
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: 3,754
|
|
Forum: Ion Torrent
07-09-2016, 04:12 AM
|
|
Replies: 3
Views: 3,754
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: 1,035
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: 1,399
|
|
Forum: Bioinformatics
01-20-2016, 09:57 AM
|
|
Replies: 0
Views: 1,945
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: 1,724
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: 3,842
|
|
Forum: Bioinformatics
12-07-2015, 08:16 AM
|
|
Replies: 4
Views: 2,379
|
|
Forum: Bioinformatics
12-07-2015, 07:34 AM
|
|
Replies: 4
Views: 2,379
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: 2,379
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...
|
