User: Abdul Rafay Khan

Reputation:
740
Status:
Trusted
Location:
Karachi, PK
Last seen:
2 days, 17 hours ago
Joined:
3 years, 4 months ago
Email:
a**********@gmail.com

Contact: alrafaykhan@gmail.com

Posts by Abdul Rafay Khan

<prev • 63 results • page 1 of 7 • next >
2
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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 2 days ago by Abdul Rafay Khan740
1
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1
answer
68
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1
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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 4 days ago by Abdul Rafay Khan740 • updated 4 days ago by haro220
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2
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135
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5 follow
2
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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 weeks ago by Abdul Rafay Khan740 • updated 4 weeks ago by Selenocysteine420
1
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0
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162
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0
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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 12 weeks ago by Abdul Rafay Khan740
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238
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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 4 months ago by Abdul Rafay Khan740
0
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0
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285
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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 4 months ago by Abdul Rafay Khan740
0
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1
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406
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1
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How to calculate the coverage in targeted sequencing?
... How to calculate coverage in targeted sequencing using Lander/Waterman equation? ...
ngs snp targeted sequencing coverage written 5 months ago by Abdul Rafay Khan740 • updated 5 months ago by KVC_bioinfo300
0
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1
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315
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1
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Velvet and ABySS (de Bruijn graph Assemblers)
... Why Velvet and ABySS, the de Bruijn graph assemblers produce greater number of contigs than any other assembler? Ideally, a good assembler should generate less number of contigs. ...
de novo assembly ngs written 10 months ago by Abdul Rafay Khan740 • updated 10 months ago by mastal5111.8k
0
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0
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284
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Ray vs other de novo assembler
... Why Ray assembler takes more time to assemble reads as compare to other de novo assembler like ABySS, Velvet, SGA or PERGA? ...
de novo assembly ngs illumina written 12 months ago by Abdul Rafay Khan740
0
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503
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Genome fraction / Genome coverage
... What is the difference between Genome fraction and Genome coverage while aligning contigs on reference genome in de novo genome assembly? ...
de novo ngs written 12 months ago by Abdul Rafay Khan740

Latest awards to Abdul Rafay Khan

Great Question 4 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Epic Question 10 months ago, created a question with more than 10,000 views. For Install and Run R on Linux
Popular Question 10 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 10 months ago, created a question with more than 1,000 views. For Best tool for Quality Assessment for Next Generation Sequencing Data?
Student 10 months ago, asked a question with at least 3 up-votes. For Why not Windows
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Gene list for an organism
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What are chimeric reads?
Student 13 months ago, asked a question with at least 3 up-votes. For .seq and .reads format?
Student 13 months ago, asked a question with at least 3 up-votes. For Why not Windows
Student 13 months ago, asked a question with at least 3 up-votes. For Bioinformatics Journal with no publishing fees?
Student 13 months ago, asked a question with at least 3 up-votes. For Bioinformatics Journal with no publishing fees?
Scholar 14 months ago, created an answer that has been accepted. For A: MaSuRCA Assembler runCA Error
Great Question 14 months ago, created a question with more than 5,000 views. For Install and Run R on Linux
Popular Question 17 months ago, created a question with more than 1,000 views. For Bowtie2 vs Tophat Whats the difference
Popular Question 17 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Bioinformatics Journal with no publishing fees?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Best Variation Analysis Software which can support VCF file Format?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Install and Run R on Linux
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Bioinformatics Journal with no publishing fees?

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