User: esraesmeray1990

Reputation:
10
Status:
New User
Location:
Izmir Biomedicine and Genome Center
Last seen:
3 months, 1 week ago
Joined:
2 years, 8 months ago
Email:
e**************@gmail.com

Posts by esraesmeray1990

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
155
views
0
answers
Best Tool for Tumor Cell Percentage Calculation (Paired NGS data)
... Hi, I am searching a tool for calculation tumor cell percentage using NGS (targeted seq.) paired end data. Most of the tools are for microarray data such as qpure tool. Could you give an advice for it? Thanks. ...
ngs next-gen snp written 5 months ago by esraesmeray199010
0
votes
2
answers
1.9k
views
2
answers
Comment: A: Is there any way to convert ENST to HGNC symbol?
... You should try bioMart package at R. ...
written 7 months ago by esraesmeray199010
0
votes
1
answer
1.1k
views
1
answers
Comment: C: GATK Panel Of Normals (PoN)
... when I tried -V again error occurs: A USER ERROR has occurred: Argument '[V, variant]' cannot be specified more than once. Also when I try new syntax : Step 1. Run Mutect2 in tumor-only mode for each normal sample: $gatk Mutect2 -R Ref.fasta -I normal1.bam -O normal1.vcf.gz $gatk Mutect2 - ...
written 7 months ago by esraesmeray199010
0
votes
1
answer
1.1k
views
1
answers
Comment: A: GATK Panel Of Normals (PoN)
... Hi i am taking the same warning aswell but it does not work (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_CreateSomaticPanelOfNormals.php ). And i also find a lot of version of CreateSomaticPanelOfNormal. I am using gatk- ...
written 7 months ago by esraesmeray199010
0
votes
0
answers
324
views
0
answers
gatk AnalyzeCovariates The following object is masked from package stats
... Hi I am tryin to use gatk AnalyzeCovariates and compare outpıuts of 2 pass using folloging code: gatk AnalyzeCovariates --before-report-file sample_addRG.recal_pass1.tabl --after-report-file sample_addRG.recal_pass2.tabl --plots-report-file sample.output.pdf But it gives following error. ...
R analyzecovariates stats gatk written 10 months ago by esraesmeray199010
0
votes
0
answers
363
views
0
answers
Comment: C: defuse running error message
... Hi, I tried but it gives the same error :( defuse_run.pl -d ~/dataset_directory -1 read1.fq.gz -2 read2.fq.gz -o output_dir ...
written 10 months ago by esraesmeray199010
0
votes
0
answers
363
views
0
answers
Comment: C: defuse running error message
... I used anaconda to install defuse: esra@asus:~$ conda install -c dranew defuse Yes defuse.cdna.fa is in dataset_directory and files are not empty. Download the Reference Dataset: esra@asus:~$ defuse_create_ref.pl -d dataset_directory esra@asus:~/dataset_directory$ ls defuse ...
written 10 months ago by esraesmeray199010
1
vote
0
answers
363
views
0
answers
defuse running error message
... I am trying to run defuse tool but ı am taking following error message i am kind of new so i really dont understand what is the probem. If anyone help me i will be appreciate . esra@asus:/media/esra/Data$ defuse_run.pl -d dataset_directory -1 read1.fq.gz -2 read2.fq.gz -o output_dir ...
software error defuse written 10 months ago by esraesmeray199010
2
votes
1
answer
2.8k
views
1
answer
conda Solving environment: failed
... Hi I am trying to install defuse and chimerascan using conda but everytime i am taking following errors: conda install -c dranew defuse Solving environment: failed UnsatisfiableError: The following specifications were found to be in conflict: - defuse -> r=3.3.2 - ...
defuse chimerascan anaconda conda written 10 months ago by esraesmeray199010 • updated 10 months ago by Devon Ryan93k
0
votes
0
answers
248
views
0
answers
Comment: C: why FastQC tool K-mer content parameter is absent?
... It seems easy but if you don't know the reason it would be a big problem, the problem is solved thank you a lot. ...
written 10 months ago by esraesmeray199010

Latest awards to esraesmeray1990

Popular Question 6 months ago, created a question with more than 1,000 views. For conda Solving environment: failed

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 720 users visited in the last hour