User: Abdul Rafay Khan
Abdul Rafay Khan • 810
- Reputation:
- 810
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- Karachi, PK
- Last seen:
- 1 month ago
- Joined:
- 3 years, 7 months ago
- Email:
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Contact: alrafaykhan@gmail.com
Posts by Abdul Rafay Khan
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0
votes
1
answer
90
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1
answers
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 Khan • 810
0
votes
1
answer
90
views
1
answer
... 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
& ...
written 4 weeks ago by
Abdul Rafay Khan • 810
• updated
4 weeks ago by
dariober ♦ 9.1k
0
votes
0
answers
151
views
0
answers
... 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 ...
written 12 weeks ago by
Abdul Rafay Khan • 810
2
votes
0
answers
217
views
0
answers
... Looking for a book which covers all aspect of Next-Generation Sequencing Data Analysis and can be add in academic course for students. ...
written 12 weeks ago by
Abdul Rafay Khan • 810
2
votes
1
answer
227
views
1
answer
... I want to align my uBAM files using bwa mem.
Does BWA mem works with uBAM files?
...
written 3 months ago by
Abdul Rafay Khan • 810
1
vote
1
answer
141
views
1
answer
... Is there any way to calculate the mean coverage of each amplicon in a whole run (in 16 or 32 samples)? ...
written 3 months ago by
Abdul Rafay Khan • 810
• updated
3 months ago by
haro • 220
4
votes
2
answers
234
views
5 follow
2
answers
... > 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 ...
written 4 months ago by
Abdul Rafay Khan • 810
• updated
4 months ago by
Selenocysteine • 460
1
vote
0
answers
208
views
0
answers
... 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? ...
written 6 months ago by
Abdul Rafay Khan • 810
1
vote
0
answers
309
views
0
answers
... 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? ...
written 7 months ago by
Abdul Rafay Khan • 810
0
votes
0
answers
414
views
0
answers
... 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 ...
written 7 months ago by
Abdul Rafay Khan • 810
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
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 What does Read Depth mean in Torrent Browser Analysis Report? Why it is shown as blank after complete sequencing?
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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