User: Abdul Rafay Khan

Reputation:
810
Status:
Trusted
Location:
Karachi, PK
Last seen:
1 month ago
Joined:
3 years, 7 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 weeks ago by Abdul Rafay Khan810
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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 weeks ago by Abdul Rafay Khan810 • updated 4 weeks ago by dariober9.1k
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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 12 weeks ago by Abdul Rafay Khan810
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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 12 weeks ago by Abdul Rafay Khan810
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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 3 months ago by Abdul Rafay Khan810
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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 3 months ago by Abdul Rafay Khan810 • updated 3 months ago by haro220
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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 4 months ago by Abdul Rafay Khan810 • updated 4 months ago by Selenocysteine460
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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 6 months ago by Abdul Rafay Khan810
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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 7 months ago by Abdul Rafay Khan810
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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 7 months ago by Abdul Rafay Khan810

Latest awards to Abdul Rafay Khan

Appreciated 12 weeks ago, created a post with more than 5 votes. For Tools to merge overlapping paired-end reads
Great Question 12 weeks ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Great Question 3 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Great Question 7 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Epic Question 13 months ago, created a question with more than 10,000 views. For Install and Run R on Linux
Popular Question 13 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 13 months ago, created a question with more than 1,000 views. For Best tool for Quality Assessment for Next Generation Sequencing Data?
Student 13 months ago, asked a question with at least 3 up-votes. For Why not Windows
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Gene list for an organism
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: What are chimeric reads?
Student 17 months ago, asked a question with at least 3 up-votes. For .seq and .reads format?
Student 17 months ago, asked a question with at least 3 up-votes. For Why not Windows
Student 17 months ago, asked a question with at least 3 up-votes. For Bioinformatics Journal with no publishing fees?
Student 17 months ago, asked a question with at least 3 up-votes. For Bioinformatics Journal with no publishing fees?
Scholar 17 months ago, created an answer that has been accepted. For A: MaSuRCA Assembler runCA Error
Great Question 17 months ago, created a question with more than 5,000 views. For Install and Run R on Linux
Popular Question 20 months ago, created a question with more than 1,000 views. For Bowtie2 vs Tophat Whats the difference
Popular Question 20 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Bioinformatics Journal with no publishing fees?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Best Variation Analysis Software which can support VCF file Format?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Install and Run R on Linux
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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