User: Abdul Rafay Khan

Reputation:
860
Status:
Trusted
Location:
Karachi, PK
Last seen:
2 months, 4 weeks ago
Joined:
3 years, 10 months ago
Email:
a**********@gmail.com

Contact: alrafaykhan@gmail.com

Posts by Abdul Rafay Khan

<prev • 67 results • page 1 of 7 • next >
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Comment: C: GATK gradlew bundle Error
... Thank you dariober, it works sudo apt-get update sudo apt-get install openjdk-8-jdk sudo update-alternatives --config java sudo update-alternatives --config javac and enter the number for which JDK to use of your choice. ...
written 4 months ago by Abdul Rafay Khan860
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GATK gradlew bundle Error
... While building gatk sudo ./gradlew bundle > Downloading > https://services.gradle.org/distributions/gradle-3.1-bin.zip > > Exception in thread "main" javax.net.ssl.SSLException: > java.security.ProviderException: java.security.InvalidKeyException: EC > parameters error at & ...
software error gatk written 4 months ago by Abdul Rafay Khan860 • updated 4 months ago by dariober9.3k
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GATK (Cannot find '.git' directory)
... Issue while Building GATK4 sudo ./gradlew bundle Starting a Gradle Daemon, 1 incompatible and 1 stopped Daemons could not be reused, use --status for details FAILURE: Build failed with an exception. Where: Build file '/home/rafay/gatk-4.0.2.0/build.gradle' line: 289 What went wrong: A problem oc ...
gatk written 5 months ago by Abdul Rafay Khan860
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Best book for learning Next-Generation Sequencing Data Analysis?
... Looking for a book which covers all aspect of Next-Generation Sequencing Data Analysis and can be add in academic course for students. ...
ngs written 5 months ago by Abdul Rafay Khan860
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Does BWA mem work with uBAM file?
... I want to align my uBAM files using bwa mem. Does BWA mem works with uBAM files? ...
ubam bwa mem bwa align written 6 months ago by Abdul Rafay Khan860
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Mean coverage in Ion Torrent PGM
... Is there any way to calculate the mean coverage of each amplicon in a whole run (in 16 or 32 samples)? ...
ion torrent ngs coverage written 6 months ago by Abdul Rafay Khan860 • updated 6 months ago by haro230
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Python script error
... > File "dna2prot2-working-test-Copy.py", line 29, in print > (entry.seq).translate()#This will translate nucleotide sequence to > amino acid sequence AttributeError: 'NoneType' object has no attribute > 'translate' Code: import sys from Bio import SeqIO f ...
python biopython written 7 months ago by Abdul Rafay Khan860 • updated 7 months ago by Selenocysteine500
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De novo sequencing?
... Why do we required de novo sequencing if almost all the organisms are being sequenced? Why Don't we only focus on reference based sequencing? ...
de novo sequencing written 9 months ago by Abdul Rafay Khan860
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Questions related assembly algorithms?
... 1) What is the overarching challenges in the assembly algorithms? 2) How different algorithms handle local repeats or segmentation duplicates in the genome? 3) How do DBG, OLC, string graph, greedy and hybrid algorithms perform with different sequencing read length? ...
olc assembly ngs dbg illumina written 10 months ago by Abdul Rafay Khan860
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ABySS and Velvet "number of contigs and contig length in pair-end and single-end datasets"
... I have run Velvet and ABySS using default parameters on my pair-end and single-end datasets, I have two questions related to the generated contigs. 1. Why Velvet has excess number of contigs in pair-end case compared to single-end? 2. Why the N50 contig length of single-end reads usin ...
illumina ngs abyss velvet written 10 months ago by Abdul Rafay Khan860

Latest awards to Abdul Rafay Khan

Scholar 12 weeks ago, created an answer that has been accepted. For A: MaSuRCA Assembler runCA Error
Supporter 12 weeks ago, voted at least 25 times.
Great Question 4 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Popular Question 4 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Appreciated 5 months ago, created a post with more than 5 votes. For Tools to merge overlapping paired-end reads
Great Question 5 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Great Question 6 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Great Question 10 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Epic Question 16 months ago, created a question with more than 10,000 views. For Install and Run R on Linux
Popular Question 16 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 16 months ago, created a question with more than 1,000 views. For Best tool for Quality Assessment for Next Generation Sequencing Data?
Student 16 months ago, asked a question with at least 3 up-votes. For Why not Windows
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Gene list for an organism
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: What are chimeric reads?
Student 20 months ago, asked a question with at least 3 up-votes. For .seq and .reads format?
Student 20 months ago, asked a question with at least 3 up-votes. For Why not Windows
Student 20 months ago, asked a question with at least 3 up-votes. For Bioinformatics Journal with no publishing fees?
Student 20 months ago, asked a question with at least 3 up-votes. For Bioinformatics Journal with no publishing fees?
Scholar 20 months ago, created an answer that has been accepted. For A: MaSuRCA Assembler runCA Error
Great Question 20 months ago, created a question with more than 5,000 views. For Install and Run R on Linux
Popular Question 23 months ago, created a question with more than 1,000 views. For Bowtie2 vs Tophat Whats the difference
Popular Question 23 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Bioinformatics Journal with no publishing fees?

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